Targeted pharmacological therapeutics in uveal melanoma

ABSTRACT

The present disclosure relates generally to methods and compositions for inhibiting or protecting against diseases arising from constitutively active G protein. In particular, the disclosure provides administration of FR900359, YM-254890 or a derivative thereof to down-regulate constitutively active Gα signaling, and is therefore useful in treatment for uveal melanoma, growth hormone-secreting pituitary tumors, tumors derived from Nevus of Ota, certain forms of other cancers (e.g. colon, lung, adenocarcinoma, skin melanoma, thyroid adenomas), cholera, Sturge-Weber Syndrome and other disorders.

FIELD OF THE INVENTION

The present disclosure relates generally to methods and compositions for treatment of diseases arising from constitutively active G protein signaling. In particular, the disclosed compositions and methods can comprise administering an FR900359, YM-254890 or a derivative thereof to a subject in need. Further, the disclosure provides administration of FR900359, YM-254890 or a derivative thereof to down-regulate constitutively active Gαq signaling, therefore useful in treatment for uveal melanoma, growth hormone-secreting pituitary tumors, tumors derived from Nevus of Ota, certain forms of other cancers (e.g. colon, lung, adenocarcinoma, skin melanoma, thyroid adenomas), cholera, Sturge-Weber Syndrome and other disorders.

BACKGROUND

A plethora of extracellular stimuli mediate cellular activity through G protein-coupled receptors, a large family of cell surface signaling molecules. The ability of G protein-coupled receptors to transduce signaling typically is induced by the binding of an appropriate ligand, resulting in a conformational change of the receptor and the subsequent interaction with the heterotrimeric αβγ guanine nucleotide-binding proteins (G proteins). G proteins located at the cytoplasmic face of the plasma membrane suffice to receive, interpret and route these signals to diverse sets of downstream target proteins. Mutations in the G protein-coupled receptors and/or G protein subunits can result in constitutively active mutants having the capacity to activate the G protein signaling cascade even in the absence of ligand. Constitutively active G protein α-subunits cause cancer, cholera, Sturge-Weber Syndrome and other disorders. While inhibitors of individual signaling pathways downstream of Ga are being studied in clinical trials, all have failed thus far. Therapeutic intervention by targeted inhibition of constitutively active Gαq subunits has yet to be achieved.

Thus, there is a need for methods which allow for targeted intervention of aberrant G protein signaling. Additionally, there is a need for methods with inhibit or reduce diseases associated with constitutively active G protein signaling.

SUMMARY

Among the various aspects of the present disclosure provide methods and pharmaceutical compositions comprising an effective amount of a constitutively active Ga subunit inhibitor, for use in treating conditions associated with constitutively active G protein signaling.

In an aspect of the disclosure provides a method of treating or preventing uveal melanoma tumor cell proliferation, the method comprising contacting uveal melanoma cells with a therapeutically effective amount of a Ga subunit inhibitor.

The present invention further provides a method of re-differentiating uveal melanoma tumor cells, the method comprising contacting uveal melanoma cells with a therapeutically effective amount of a Ga subunit inhibitor. In an aspect of the disclosure is a method of inducing polycomb repressive complex-2 mediated gene repression in uveal melanoma cells.

In a further aspect of the invention provides a method of locking a constitutively active guanine nucleotide-binding protein in a GDP-bound state. In a further aspect of the invention provides inhibiting downstream signaling pathways that result from constitutively active guanine nucleotide-binding proteins.

In certain embodiments, the Ga subunit inhibitor is selected from the group consisting of FR900359, YM-254890, a salt, prodrug or solvate thereof, an analog thereof, a derivative thereof, and any combinations thereof.

While multiple embodiments are disclosed, still other embodiments of the present invention will become apparent to those skilled in the art from the following detailed description, which shows and describes illustrative embodiments of the invention. Accordingly, the figures and detailed description are to be regarded as illustrative in nature and not restrictive.

BRIEF DESCRIPTION OF THE FIGURES

The application file contains at least one drawing executed in color. Copies of this patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1A, FIG. 1B, FIG. 1C and FIG. 1D shows FR traps mutant constitutively active Gαq in the inactive GDP-bound state. (FIG. 1A-1C) depicts the effect of FR on the activity state of Gα subunits as determined by interaction with Gβγ or RGS domains in split luciferase complementation assays. FIG. 1A Effect of FR on interaction of Gβγ2 with the indicated wild type (WT) or mutant constitutively active (Q/L) forms of Gα (q) or Gα13 (13). * p<0.01; ** p<0.05. FIG. 1B Potency of FR as a driver of interaction of Gβγ2 with wild type or mutant constitutively active Gαq. FIG. 1C Potency of FR as inhibitor of interaction of RGS2 with mutant constitutively active (Q/L) Gαq, or interaction of the RGS domain of LARG (LARG-RGS) with mutant constitutively active Gα13. FIG. 1D Potency of FR as inhibitor of signal transduction by constitutively active Gαq or Gα13 detected with an SRE(L) promoter-driven transcriptional reporter. Constitutively active Gαq (Q/L), constitutively active Gαq bearing the indicated FR binding site mutations, and constitutively Gα13 (Q/L) were studied.

FIG. 2A, FIG. 2B and FIG. 2C displays engineering an optimized FR binding site in FR-insensitive Gαi1 is sufficient to confer FR sensitivity. FIG. 2A Amino acid residues in Gαi1 identical to or diverged from the FR/YM binding site in Gαq are indicated in green and red, respectively. An FR/YM binding site was created in Gαi1 by introducing the eight indicated amino acid substitutions so as to match the corresponding residues of Gαq, thereby producing a chimeric Gα subunit termed Gi/q. FIG. 2B Effect of FR on guanine nucleotide exchange in vitro by Gi/q α-subunits or a mutant (R54K) corresponding to a Gαq mutant that is less sensitive to FR/YM. FIG. 2C Effect of FR on agonist-evoked signaling mediated by Gi/q. Inhibition of forskolin-induced cAMP formation by Gi-coupled cannabinoid receptors was measured in Neuro2A cells transfected with a cAMP FRET reporter and pertussis toxin (PTX)-resistant and EE epitope-tagged forms of the indicated Gα subunits, and treated with PTX to inactivate endogenously expressed Gi. Inhibition of forskolin-induced cAMP formation by a cannabinoid receptor agonist (WIN 55, 212-2; WIN) was measured by FRET. Attenuation of this inhibitory effect by FR was quantified relative to vehicle controls. **p<0.05; *p<0.01.

FIG. 3A and FIG. 3B shows FR inhibits signaling by constitutively active Gαq in UM cells. Inhibition of signaling by constitutively active Gαq in UM cultured cell lines was quantified by measuring intracellular inositol 1-phosphate (IP1), a metabolically stable product of inositol 1,4,5-trisphosphate produced by Gαq-stimulated phospholipase Cβ. FIG. 3A Basal IP1 levels in UM cell lines driven by constitutively active Gαq (92.1 and Mel202) and BRAF (OCM-1A). FIG. 3B Effects of FR on IP1 levels in 92.1, Mel202 and OCM-1A cells. *p<0.01.

FIG. 4A, FIG. 4B, FIG. 4C and FIG. 4D shows FR sensitivity of growth and viability of UM cells driven by constitutively active Gαq. FIG. 4A Changes in viability of UM cells treated with FR were quantified using a water-soluble tetrazolium salt assay. The fold change in viability over time is shown for Gαq(Q209L) driven 92.1 and Mel-202 cells, and for BRAF(V600E)-driven OCM-1A cells in response to increasing concentration of FR. FIG. 4B Potency of FR as an inhibitor of UM cell viability measured as in (FIG. 4A). FIG. 4C The indicated UM cell lines were treated for 3 d with the indicated concentrations of FR and analyzed for DNA content. Flow cytometry of the Gαq(Q209L) driven cell lines (92.1 and Mel202) and BRAF(V600E)-driven OCM-treated 3 d with vehicle or FR. FIG. 4D Potency of FR as inducer of apoptosis (sub-G1 cells) and inhibitor of cell proliferation (S- and G2/M-phase cells). *p<0.01.

FIG. 5A, FIG. 5B, and FIG. 5C shows FR induces redifferentiation of UM cells driven by constitutively active Gαq. FIG. 5A Morphological changes elicited by FR. UM cell lines were treated 3 d with FR and imaged by phase contrast microscopy. FR caused UM cells driven by constitutively active Gαq (92.1 and Mel202) to lose their characteristic spindle shaped and assume a stellate shape with multiple projections. FR had no effect on BRAF-driven UM cells (OCM-1A). FIG. 5B Melanocytic differentiation of FR-treated UM cells indicated by pigmentation. UM cell lines were treated 3 d with FR. Cells were pelleted and examined macroscopically. FIG. 5C Induction of melanocytic markers by FR as indicated by immunofluorescence staining of tyrosinase (TYR), dopachrome tautomerase (DCT) and pre-melanosomal protein (PMEL) of Gαq-mutant cell lines (92.1 and Mel202) but not BRAF-driven UM cells (OCM-1A). Scale bar=50 μm.

FIG. 6A and FIG. 6B shows effects of FR on YAP-driven gene expression. FIG. 6A FR upregulates some YAP target genes but downregulates others in Gαq(Q209L)-driven 92.1 cells. Expression data from two experimental replicates are mean-centered; the color gradient corresponds to difference in log 2 ratio of expression from the mean, such that 0.5 versus −0.5 is a total difference of 2-fold in unlogged expression. FIG. 6B Potency of FR as an inducer of a YAP-driven transcriptional reporter in Gαq(Q209L)-driven Mel202 and 92.1 cells, but not in BRAF(V600E)-driven OCM-1A cells.

FIG. 7A, FIG. 7B, FIG. 7C, FIG. 7D, FIG. 7E, FIG. 7F and FIG. 7G shows FR represses expression of differentiation genes by restoring function of the polycomb repressive complex 2. Gαq-mutant 92.1 UM cells were treated with FR or vehicle, and RNA was collected 1 and 3 d after treatment for RNA-Seq analysis. FIG. 7A Unsupervised principal component analysis identified FR treatment and time in culture as the two main separable factors contributing to changes in gene expression. FIG. 7B Volcano plot comparing gene expression between FR- and vehicle-treated samples identifies a group of significantly downregulated genes (circled) associated with FR treatment. FIG. 7C Gene ontology analysis of the FR-repressed geneset shows that most are involved in developmental processes and differentiation. FIG. 7D FR-repressed genes identified as targets of the polycomb repressive complex 2 by Geneset enrichment analysis. FIG. 7E The Ezh1/2 inhibitor GSK503 blocks the morphological differentiation elicited by FR. 92.1 UM cells were treated 7 d with GSK503 and 3 d with FR and then imaged by phase contrast microscopy. FIG. 7F GSK503 decreased pigmentation of FR-treated cells, visualized by macroscopic inspection. 92.1 cells were treated 7 d with GSK503 and 3 d with FR and pelleted. FIG. 7G PRC2 inhibition by GSK503. Immunoblots of 92.1 cells treated 7 d with GSK503 show reduced histone H3 lysine 27 trimethylation.

FIG. 8A, FIG. 8B, FIG. 8C and FIG. 8D shows FR Inhibition of Gαi1 bearing an engineered FR binding site. FIG. 8A Inhibition of nucleotide exchange in vitro. Nucleotide exchange was assayed by measuring increases in fluorescence of BODIPY-GTPγS (ΔF/Fo) upon binding to the indicated purified His-tagged Gα subunits in the absence or presence of the indicated concentrations of FR. Gαi/q contains an engineered FR binding site as illustrated in FIG. 2A. Curves are representative of three independent experiments. FIG. 8B Protein expression of internally EE epitope-tagged Gα subunits in transiently transfected N2a cells as detected by immunoblotting. Ga mutants insensitive to pertussis toxin (C351G) and/or FR (R54K) are indicated. FIG. 8C Inhibition of forskolin-evoked cAMP formation by Gαi1 bearing an engineered FR binding site. Inhibition of forskolin-evoked cAMP production by an agonist (WIN 55 212-2 (WIN)) for Gαi1-coupled type 1 cannabinoid receptors in N2a cells was used to assay function of the Gαi1 subunit bearing an engineered FR binding site. N2a cells were transfected with the indicated Gα subunits and the Epac-SH187 cAMP FRET sensor, and treated or not with pertussis toxin to inactivate endogenously expressed Gαi/o. Cells then were treated as indicated with forskolin (FSK; 20 μM; black bars) for 5 min to stimulate cAMP production, and then with WIN (5 μM; grey bars) to activate endogenous Gαi/o coupled cannabinoid type 1 receptors and inhibit adenylyl cyclase. Each transfected Gα subunit bearing the C351G substitution, including those also bearing an engineered FR binding site or an FR-resistant mutation (R54K), were functional as indicated by the ability to mediate pertussis toxin-insensitive inhibition of cAMP formation. Results shown are the averages of three independent experiments. FIG. 8D FR inhibits signaling mediated by Gαi1 bearing an FR binding site. Signaling mediated by the indicated transfected forms of Gαi1 in N2a cells treated with pertussis toxin with or without the indicated concentrations of FR was assayed as described in panel C. Forskolin (FSK; black bars) and agonist (WIN; grey bars) treatment are indicated. FR concentrations are color coded as indicated. Data from one experiment representative of three independent experiments are shown.

FIG. 9A and FIG. 9B shows heatmaps of cell cycle and apoptosis gene expression in response to FR. Expression data from two experimental replicates are mean-centered, and the colorgradient corresponds to difference in log 2 ratio of expression from the mean, such that −0.5 versus 0.5 is a total difference of 2-fold in unlogged expression. Genes are ordered by fold change of FR-treated versus control from positive (left) to negative (right). FIG. 9A FR has little overall effect on expression of cell cycle genes. FIG. 9B FR evokes modest up- and down-regulation of pro- and anti-apoptotic genes.

FIG. 10A, FIG. 10B, FIG. 10C, FIG. 10D, FIG. 10E and FIG. 10F shows validation of selected FR target genes. The results for six genes showing significant changes in expression in response to FR by RNA-Seq were validated by qPCR. ADRA2A, HAND2, SCARF2, and WT1 are known targets of PRC2-directed histone methylation and all showed significant down-regulation in response to FR in Gαq(Q209L)-driven 92.1 UM cells with no effect on BRAF(B600E)-driven OCM-1A UM cells. PMP22, a known YAP target, and DCT, a pigmentation enzyme, were significantly upregulated in response to FR in Gαq(Q209L)-driven 92.1 UM cells but showed no effect on BRAF(B600E)-driven OCM-1A UM cells.

DETAILED DESCRIPTION

The present invention provides, generally, methods and compositions for treating and preventing disorders mediated by constitutively active G-protein signaling. In particular, provided herein are compositions comprising FR900359, YM-254890 or a derivative thereof and methods of use. In particular, Applicants have surprisingly discovered that FR900359 or YM-254890 and derivatives thereof can allosterically inhibit the nucleotide exchange to trap constitutively active mutant Gα in the inactive GDP-bound state and as such represent a therapeutic option for treatment of diseases and disorders associated with constitutively active G-protein signaling. The invention is useful, in non-limiting examples, for slowing, protecting from the effects of, or halting the progression of a condition resulting from constitutively active G-protein signaling.

The present invention also provides therapeutic compositions for treating a constitutively active G-protein modulated disease in a subject, wherein the composition comprises an inhibitor of a constitutively active G-protein and a carrier. In non-limiting examples the G-protein inhibitor is FR900359, YM-254890, a salt, prodrug or solvate thereof, an analog thereof, a derivative thereof, and any combinations thereof.

Disclosed are the components to be used to prepare the disclosed compositions as well as the compositions themselves to be used within the methods disclosed herein. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular compound is disclosed and discussed and a number of modifications that can be made to a number of molecules of the compound are discussed, specifically contemplated is each and every combination and permutation of the compound and the modifications that are possible unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited each is individually and collectively contemplated meaning combinations, A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are considered disclosed. Likewise, any subset or combination of these is also disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E would be considered disclosed. This concept applies to all aspects of this application including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods.

Various aspects of the invention are described in further detail in the following sections.

(I) COMPOSITIONS

One aspect of the present disclosure provides a small molecule inhibitor of a constitutively active Gα subunit. As used herein, a small molecule inhibitor of a constitutively active Gα subunit, or “Gα subunit inhibitor” includes any compound capable of downregulating, decreasing, reducing, suppressing or inactivating the amount and/or activity of a constitutively active G-protein. In some embodiments the inhibitors for use with the invention may function to inhibit constitutively active G-protein signaling, by locking the G-protein in a GDP-bound state. Compounds that decrease the activity of a constitutively active G-protein also decrease the associated downstream signaling pathways. In alternative aspects, the invention provides compositions for targeting a constitutively active G-protein, e.g., antibodies, aptamers, inhibitory peptides, inhibitory nucleic acids and the like.

A composition of the invention may optionally comprise one or more additional drug or therapeutically active agent in addition to the FR900359, YM-254890, or derivatives thereof. A composition of the invention may further comprise a pharmaceutically acceptable excipient, carrier, or diluent. Further, a composition of the invention may contain preserving agents, solubilizing agents, stabilizing agents, wetting agents, emulsifiers, sweeteners, colorants, odorants, salts (substances of the present invention may themselves be provided in the form of a pharmaceutically acceptable salt), buffers, coating agents, or antioxidants.

Other aspects of the invention are described in further detail below.

(a) FR900359, YM-254890, and Derivatives Thereof

In general, the compounds detailed herein include compounds comprising a FR900359, structure as diagrammed below. FR900359 is a synthetic organic molecule. Its chemical elements are expressed as C₄₉H₇₅N₇O₁₅, with a molecular weight of 1002.173 g/mol. FR900359 can be isolated from the plant Ardisia crenata and its synthesis is known, for example as described by Xiong et al. Nat Chem. 2016 November; 8(11): 1035-1041, herein incorporated by reference in its entirety. FR900359 is also manufactured commercially.

FR900359 may also be called [(1S)-1-[(3S,6R,9S,12S,18R,21S,22R)-21-acetamido-18-benzyl-3-[(1S)-1-methoxyethyl]-4,9,10,12,16-pentamethyl-15-methylidene-2,5,8,11,14,17,20-heptaoxo-22-propan-2-yl-1,19-dioxa-4,7,10,13,16-pentazacyclodocos-6-yl]-2-methylpropyl] (2S,3R)-3-hydroxy-4-methyl-2-(propanoylamino)pentanoate. In some embodiments, the disclosure provides a pharmaceutical composition comprising a therapeutically effective amount of FR900359, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

Moreover, the compounds as described herein include the small molecule inhibitor is YM-254890. YM-254890 is a cyclic depsipeptide isolated from a soil bacterium Chromobacterium sp. YM-254890, has the following chemical formula:

YM-254890 is also known as (1R)-1-{(3S,6S,9S, 12S,18R,21S,22R)-21-Acetamido-18-benzyl-3-[(1R)-1-methoxyethyl]-9,10,12,16,22-pentamethyl-15-methylene-2,5,8,11,14,17,20-heptaoxo-1,19-dioxa-4,7,10,13,16-pentaazacyclodocosan-6-yl}-2-methylpropyl (2S,3R)-2-acetamido-3-hydroxy-4-methylpentanoate. YM-254890 can be synthesized, for example, as described by Xiong et al. Nat Chem. 2016 November; 8(11): 1035-1041, herein incorporated by reference in its entirety. The invention provides a pharmaceutical composition comprising an effective amount of YM-254890 or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

Provided herein are derivatives of FR900359 and YM-254890. FR900359 and YM-254890 derivatives are modified versions of FR900359 and YM-254890, respectively that are useful as an inhibitor of constitutively active G-protein signaling. As used herein an “FR900359 derivative” or “YM-254890 derivate” may be any derivative known in the art. FR900359 and YM-254890. FR900359 and YM-254890 derivatives are known in the art, including, for example as described in Zhang et al. Eur J Med Chem. 2018 Aug. 5; 156:847-860; Reher et al. Chem Med Chem. 2018 Aug. 20; 13(16):1634-1643; Zhang et al. Chem Med Chem. 2017 Jun. 7; 12(11):830-834; and Xiong et al. Nat Chem. 2016 November; 8(11): 1035-1041, herein incorporated by reference in their entirety.

(b) Components of the Composition

The present disclosure also provides pharmaceutical compositions. The pharmaceutical composition comprises FR900359, YM-254890, and derivatives thereof, as an active ingredient, and at least one pharmaceutically acceptable excipient.

The pharmaceutically acceptable excipient may be a diluent, a binder, a filler, a buffering agent, a pH modifying agent, a disintegrant, a dispersant, a preservative, a lubricant, taste-masking agent, a flavoring agent, or a coloring agent. The amount and types of excipients utilized to form pharmaceutical compositions may be selected according to known principles of pharmaceutical science.

In each of the embodiments described herein, a composition of the invention may optionally comprise one or more additional drug or therapeutically active agent in addition to FR900359, YM-254890, and derivatives thereof. Thus, in addition to the therapies described herein, one may also provide to the subject other therapies known to be efficacious for treatment of the disease, disorder, or condition. In some embodiments, the additional drug or therapeutic agent maybe a small molecule, a polypeptide, a nucleic acid, a cell or cell lysate, a virus (e.g. oncolytic virus), and antibody or the like. In some embodiments, the administration of FR900359, YM-254890, or derivatives thereof maybe administered before or after radiation or surgery. In some embodiments, the additional drug or therapeutically active agent induces anti-inflammatory effects. In some embodiments, the secondary agent is selected from a corticosteroid, a non-steroidal anti-inflammatory drug (NSAID), an intravenous immunoglobulin, a tyrosine kinase inhibitor, a fusion protein, a monoclonal antibody directed against one or more pro-inflammatory cytokines, a chemotherapeutic agent and a combination thereof. In some embodiments, agents suitable for combination therapy include but are not limited to immune checkpoint blockades. Non-limiting examples of immune checkpoint blockade agents include inhibitors of PD-1/PD-L1, CTLA-4, IDO, TIM3, LAG3, TIGIT, BTLA, VISTA, ICOS, KIRs, CD39, Pembrolizumab, Nivolumab, Ipilimumab, Atezolizumab, Avelumab, Durvalumab. In some embodiments, the additional drug or therapeutic agent is IMCgp100. In some embodiments, the additional drug or therapeutic agent is a CYSLTR2 antagonists. In one aspect, the additional drug or therapeutically active agent is a chemotherapeutic agent. In another aspect, agents suitable for combination therapy include CAR T-cell therapy. In some embodiments, the secondary agent may be a glucocorticoid, a corticosteroid, a non-steroidal anti-inflammatory drug (NSAID), a phenolic antioxidant, an anti-proliferative drug, a tyrosine kinase inhibitor, an anti IL-5 or an IL5 receptor monoclonal antibody, an anti IL-13 or an anti IL-13 receptor monoclonal antibody, an IL-4 or an IL-4 receptor monoclonal antibody, an anti IgE monoclonal antibody, a monoclonal antibody directed against one or more pro-inflammatory cytokines, a TNF-α inhibitor, a fusion protein, a chemotherapeutic agent or a combination thereof. In some embodiments, the secondary agent is an anti-inflammatory drug. In some embodiments, anti-inflammatory drugs include, but are not limited to, alclofenac, alclometasone dipropionate, algestone acetonide, alpha amylase, amcinafal, amcinafide, amfenac sodium, amiprilose hydrochloride, anakinra, anirolac, anitrazafen, apazone, balsalazide disodium, bendazac, benoxaprofen, benzydamine hydrochloride, bromelains, broperamole, budesonide, carprofen, cicloprofen, cintazone, cliprofen, clobetasol propionate, clobetasone butyrate, clopirac, cloticasone propionate, cormethasone acetate, cortodoxone, curcumin, deflazacort, desonide, desoximetasone, dexamethasone dipropionate, diclofenac potassium, diclofenac sodium, diflorasone diacetate, diflumidone sodium, diflunisal, difluprednate, diftalone, dimethyl sulfoxide, drocinonide, endrysone, enlimomab, enolicam sodium, epirizole, etodolac, etofenamate, felbinac, fenamole, fenbufen, fenclofenac, fenclorac, fendosal, fenpipalone, fentiazac, flazalone, fluazacort, flufenamic acid, flumizole, flunisolide acetate, flunixin, flunixin meglumine, fluocortin butyl, fluorometholone acetate, fluquazone, flurbiprofen, fluretofen, fluticasone propionate, furaprofen, furobufen, halcinonide, halobetasol propionate, halopredone acetate, ibufenac, ibuprofen, ibuprofen aluminum, ibuprofen piconol, ilonidap, indomethacin, indomethacin sodium, indoprofen, indoxole, intrazole, isoflupredone acetate, isoxepac, isoxicam, ketoprofen, lofemizole hydrochloride, lomoxicam, loteprednol etabonate, lysofylline, meclofenamate sodium, meclofenamic acid, meclorisone dibutyrate, mefenamic acid, mesalamine, meseclazone, methylprednisolone suleptanate, momiflumate, nabumetone, naproxen, naproxen sodium, naproxol, nimazone, olsalazine sodium, orgotein, orpanoxin, oxaprozin, oxyphenbutazone, paranyline hydrochloride, pentosan polysulfate sodium, phenbutazone sodium glycerate, piroxicam, piroxicam cinnamate, piroxicam olamine, pirprofen, prednazate, prifelone, prodolic acid, proquazone, proxazole, proxazole citrate, rimexolone, romazarit, salcolex, salnacedin, salsalate, sanguinarium chloride, seclazone, sermetacin, sudoxicam, sulindac, suprofen, talmetacin, talniflumate, talosalate, tebufelone, tenidap, tenidap sodium, tenoxicam, tesicam, tesimide, tetrydamine, tiopinac, tixocortol pivalate, tolmetin, tolmetin sodium, triclonide, triflumidate, zidometacin, zomepirac sodium, aspirin (acetylsalicylic acid), salicylic acid, corticosteroids, glucocorticoids, tacrolimus, pimecorlimus, mepolizumab, prodrugs thereof, and a combination thereof.

(i) Diluent

In one embodiment, the excipient may be a diluent. The diluent may be compressible (i.e., plastically deformable) or abrasively brittle. Non-limiting examples of suitable compressible diluents include microcrystalline cellulose (MCC), cellulose derivatives, cellulose powder, cellulose esters (i.e., acetate and butyrate mixed esters), ethyl cellulose, methyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, sodium carboxymethylcellulose, corn starch, phosphated corn starch, pregelatinized corn starch, rice starch, potato starch, tapioca starch, starch-lactose, starch-calcium carbonate, sodium starch glycolate, glucose, fructose, lactose, lactose monohydrate, sucrose, xylose, lactitol, mannitol, malitol, sorbitol, xylitol, maltodextrin, and trehalose. Non-limiting examples of suitable abrasively brittle diluents include dibasic calcium phosphate (anhydrous or dihydrate), calcium phosphate tribasic, calcium carbonate, and magnesium carbonate.

(ii) Binder

In another embodiment, the excipient may be a binder. Suitable binders include, but are not limited to, starches, pregelatinized starches, gelatin, polyvinylpyrrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C₁₂-C₁₈ fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, polypeptides, oligopeptides, and combinations thereof.

(iii) Filler

In another embodiment, the excipient may be a filler. Suitable fillers include, but are not limited to, carbohydrates, inorganic compounds, and polyvinylpyrrolidone. By way of non-limiting example, the filler may be calcium sulfate, both di- and tri-basic, starch, calcium carbonate, magnesium carbonate, microcrystalline cellulose, dibasic calcium phosphate, magnesium carbonate, magnesium oxide, calcium silicate, talc, modified starches, lactose, sucrose, mannitol, or sorbitol.

(iv) Buffering Agent

In still another embodiment, the excipient may be a buffering agent. Representative examples of suitable buffering agents include, but are not limited to, phosphates, carbonates, citrates, tris buffers, and buffered saline salts (e.g., Tris buffered saline or phosphate buffered saline).

(v) pH Modifier

In various embodiments, the excipient may be a pH modifier. By way of non-limiting example, the pH modifying agent may be sodium carbonate, sodium bicarbonate, sodium citrate, citric acid, or phosphoric acid.

(vi) Disintegrant

In a further embodiment, the excipient may be a disintegrant. The disintegrant may be non-effervescent or effervescent. Suitable examples of non-effervescent disintegrants include, but are not limited to, starches such as corn starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, gums such as agar, guar, locust bean, karaya, pecitin, and tragacanth. Non-limiting examples of suitable effervescent disintegrants include sodium bicarbonate in combination with citric acid and sodium bicarbonate in combination with tartaric acid.

(vii) Dispersant

In yet another embodiment, the excipient may be a dispersant or dispersing enhancing agent. Suitable dispersants may include, but are not limited to, starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and microcrystalline cellulose.

(viii) Excipient

In another alternate embodiment, the excipient may be a preservative. Non-limiting examples of suitable preservatives include antioxidants, such as BHA, BHT, vitamin A, vitamin C, vitamin E, or retinyl palmitate, citric acid, sodium citrate; chelators such as EDTA or EGTA; and antimicrobials, such as parabens, chlorobutanol, or phenol.

(ix) Lubricant

In a further embodiment, the excipient may be a lubricant. Non-limiting examples of suitable lubricants include minerals such as talc or silica; and fats such as vegetable stearin, magnesium stearate, or stearic acid.

(x) Taste-Masking Agent

In yet another embodiment, the excipient may be a taste-masking agent. Taste-masking materials include cellulose ethers; polyethylene glycols; polyvinyl alcohol; polyvinyl alcohol and polyethylene glycol copolymers; monoglycerides or triglycerides; acrylic polymers; mixtures of acrylic polymers with cellulose ethers; cellulose acetate phthalate; and combinations thereof.

(xi) Flavoring Agent

In an alternate embodiment, the excipient may be a flavoring agent. Flavoring agents may be chosen from synthetic flavor oils and flavoring aromatics and/or natural oils, extracts from plants, leaves, flowers, fruits, and combinations thereof.

(xii) Coloring Agent

In still a further embodiment, the excipient may be a coloring agent. Suitable color additives include, but are not limited to, food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), or external drug and cosmetic colors (Ext. D&C).

The weight fraction of the excipient or combination of excipients in the composition may be about 99% or less, about 97% or less, about 95% or less, about 90% or less, about 85% or less, about 80% or less, about 75% or less, about 70% or less, about 65% or less, about 60% or less, about 55% or less, about 50% or less, about 45% or less, about 40% or less, about 35% or less, about 30% or less, about 25% or less, about 20% or less, about 15% or less, about 10% or less, about 5% or less, about 2%, or about 1% or less of the total weight of the composition.

The agents and compositions described herein can be formulated by any conventional manner using one or more pharmaceutically acceptable carriers or excipients as described in, for example, Remington's Pharmaceutical Sciences (A. R. Gennaro, Ed.), 21st edition, ISBN: 0781746736 (2005), incorporated herein by reference in its entirety. Such formulations will contain a therapeutically effective amount of a biologically active agent described herein, which can be in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the subject.

The term “formulation” refers to preparing a drug in a form suitable for administration to a subject, such as a human. Thus, a “formulation” can include pharmaceutically acceptable excipients, including diluents or carriers.

The term “pharmaceutically acceptable” as used herein can describe substances or components that do not cause unacceptable losses of pharmacological activity or unacceptable adverse side effects. Examples of pharmaceutically acceptable ingredients can be those having monographs in United States Pharmacopeia (USP 29) and National Formulary (NF 24), United States Pharmacopeial Convention, Inc, Rockville, Md., 2005 (“USP/NF”), or a more recent edition, and the components listed in the continuously updated Inactive Ingredient Search online database of the FDA. Other useful components that are not described in the USP/NF, etc. may also be used.

The term “pharmaceutically acceptable excipient,” as used herein, can include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic, or absorption delaying agents. The use of such media and agents for pharmaceutical active substances is well known in the art (see generally Remington's Pharmaceutical Sciences (A. R. Gennaro, Ed.), 21st edition, ISBN: 0781746736 (2005)). Except insofar as any conventional media or agent is incompatible with an active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

A “stable” formulation or composition can refer to a composition having sufficient stability to allow storage at a convenient temperature, such as between about 0° C. and about 60° C., for a commercially reasonable period of time, such as at least about one day, at least about one week, at least about one month, at least about three months, at least about six months, at least about one year, or at least about two years.

The formulation should suit the mode of administration. The agents of use with the current disclosure can be formulated by known methods for administration to a subject using several routes which include, but are not limited to, parenteral, pulmonary, oral, topical, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, ophthalmic, buccal, and rectal. The individual agents may also be administered in combination with one or more additional agents or together with other biologically active or biologically inert agents. Such biologically active or inert agents may be in fluid or mechanical communication with the agent(s) or attached to the agent(s) by ionic, covalent, Van der Waals, hydrophobic, hydrophilic or other physical forces.

Controlled-release (or sustained-release) preparations may be formulated to extend the activity of the agent(s) and reduce dosage frequency. Controlled-release preparations can also be used to effect the time of onset of action or other characteristics, such as blood levels of the agent, and consequently affect the occurrence of side effects. Controlled-release preparations may be designed to initially release an amount of an agent(s) that produces the desired therapeutic effect, and gradually and continually release other amounts of the agent to maintain the level of therapeutic effect over an extended period of time. In order to maintain a near-constant level of an agent in the body, the agent can be released from the dosage form at a rate that will replace the amount of agent being metabolized or excreted from the body. The controlled-release of an agent may be stimulated by various inducers, e.g., change in pH, change in temperature, enzymes, water, or other physiological conditions or molecules.

(d) Administration

(i) Dosage Forms

The composition can be formulated into various dosage forms and administered by a number of different means that will deliver a therapeutically effective amount of the active ingredient. Such compositions can be administered orally (e.g. inhalation), parenterally, or topically in dosage unit formulations containing conventional nontoxic pharmaceutically acceptable carriers, adjuvants, and vehicles as desired. Topical administration may also involve the use of transdermal administration such as transdermal patches or iontophoresis devices. The term parenteral as used herein includes subcutaneous, intravenous, intramuscular, intra-articular, or intrasternal injection, or infusion techniques. Formulation of drugs is discussed in, for example, Gennaro, A. R., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. (18th ed, 1995), and Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Dekker Inc., New York, N.Y. (1980). In a specific embodiment, a composition may be a food supplement or a composition may be a cosmetic.

Solid dosage forms for oral administration include capsules, tablets, caplets, pills, powders, pellets, and granules. In such solid dosage forms, the active ingredient is ordinarily combined with one or more pharmaceutically acceptable excipients, examples of which are detailed above. Oral preparations may also be administered as aqueous suspensions, elixirs, or syrups. For these, the active ingredient may be combined with various sweetening or flavoring agents, coloring agents, and, if so desired, emulsifying and/or suspending agents, as well as diluents such as water, ethanol, glycerin, and combinations thereof. For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

For parenteral administration (including subcutaneous, intraocular, intradermal, intravenous, intramuscular, intra-articular and intraperitoneal), the preparation may be an aqueous or an oil-based solution. Aqueous solutions may include a sterile diluent such as water, saline solution, a pharmaceutically acceptable polyol such as glycerol, propylene glycol, or other synthetic solvents; an antibacterial and/or antifungal agent such as benzyl alcohol, methyl paraben, chlorobutanol, phenol, thimerosal, and the like; an antioxidant such as ascorbic acid or sodium bisulfite; a chelating agent such as etheylenediaminetetraacetic acid; a buffer such as acetate, citrate, or phosphate; and/or an agent for the adjustment of tonicity such as sodium chloride, dextrose, or a polyalcohol such as mannitol or sorbitol. The pH of the aqueous solution may be adjusted with acids or bases such as hydrochloric acid or sodium hydroxide. Oil-based solutions or suspensions may further comprise sesame, peanut, olive oil, or mineral oil. The compositions may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carried, for example water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules, and tablets.

For topical (e.g., transdermal or transmucosal) administration, penetrants appropriate to the barrier to be permeated are generally included in the preparation. Pharmaceutical compositions adapted for topical administration may be formulated as ointments, creams, suspensions, lotions, powders, solutions, pastes, gels, sprays, aerosols, or oils. In some embodiments, the pharmaceutical composition is applied as a topical ointment or cream. When formulated in an ointment, the active ingredient may be employed with either a paraffinic or a water-miscible ointment base. Alternatively, the active ingredient may be formulated in a cream with an oil-in-water cream base or a water-in-oil base. Pharmaceutical compositions adapted for topical administration to the eye include eye drops wherein the active ingredient is dissolved or suspended in a suitable carrier, especially an aqueous solvent. Pharmaceutical compositions adapted for topical administration in the mouth include lozenges, pastilles, and mouth washes. Transmucosal administration may be accomplished through the use of nasal sprays, aerosol sprays, tablets, or suppositories, and transdermal administration may be via ointments, salves, gels, patches, or creams as generally known in the art.

In certain embodiments, a composition comprising the FR900359, YM-254890, or derivatives thereof, is encapsulated in a suitable vehicle to either aid in the delivery of the compound to target cells, to increase the stability of the composition, or to minimize potential toxicity of the composition. As will be appreciated by a skilled artisan, a variety of vehicles are suitable for delivering a composition of the present invention. Non-limiting examples of suitable structured fluid delivery systems may include nanoparticles, liposomes, microemulsions, micelles, dendrimers, and other phospholipid-containing systems. Methods of incorporating compositions into delivery vehicles are known in the art.

In one alternative embodiment, a liposome delivery vehicle may be utilized. Liposomes, depending upon the embodiment, are suitable for delivery of the FR900359, YM-254890, or derivatives thereof, in view of their structural and chemical properties. Generally speaking, liposomes are spherical vesicles with a phospholipid bilayer membrane. The lipid bilayer of a liposome may fuse with other bilayers (e.g., the cell membrane), thus delivering the contents of the liposome to cells. In this manner, the the FR900359, YM-254890, or derivatives thereof may be selectively delivered to a cell by encapsulation in a liposome that fuses with the targeted cell's membrane.

Liposomes may be comprised of a variety of different types of phosolipids having varying hydrocarbon chain lengths. Phospholipids generally comprise two fatty acids linked through glycerol phosphate to one of a variety of polar groups. Suitable phospholids include phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). The fatty acid chains comprising the phospholipids may range from about 6 to about 26 carbon atoms in length, and the lipid chains may be saturated or unsaturated. Suitable fatty acid chains include (common name presented in parentheses) n-dodecanoate (laurate), n-tretradecanoate (myristate), n-hexadecanoate (palm itate), n-octadecanoate (stearate), n-eicosanoate (arachidate), n-docosanoate (behenate), n-tetracosanoate (lignocerate), cis-9-hexadecenoate (palmitoleate), cis-9-octadecanoate (oleate), cis,cis-9,12-octadecandienoate (linoleate), all cis-9, 12, 15-octadecatrienoate (linolenate), and all cis-5,8,11,14-eicosatetraenoate (arachidonate). The two fatty acid chains of a phospholipid may be identical or different. Acceptable phospholipids include dioleoyl PS, dioleoyl PC, distearoyl PS, distearoyl PC, dimyristoyl PS, dimyristoyl PC, dipalmitoyl PG, stearoyl, oleoyl PS, palmitoyl, linolenyl PS, and the like.

The phospholipids may come from any natural source, and, as such, may comprise a mixture of phospholipids. For example, egg yolk is rich in PC, PG, and PE, soy beans contains PC, PE, PI, and PA, and animal brain or spinal cord is enriched in PS. Phospholipids may come from synthetic sources too. Mixtures of phospholipids having a varied ratio of individual phospholipids may be used. Mixtures of different phospholipids may result in liposome compositions having advantageous activity or stability of activity properties. The above mentioned phospholipids may be mixed, in optimal ratios with cationic lipids, such as N-(1-(2,3-dioleolyoxy)propyl)-N,N,N-trimethyl ammonium chloride, 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchloarate, 3,3′-deheptyloxacarbocyanine iodide, 1,1′-dedodecyl-3,3,3′,3′-tetramethylindocarbocyanine perchloarate, 1,1′-dioleyl-3, 3, 3′,3′-tetramethylindo carbocyanine methanesulfonate, N-4-(delinoleylaminostyryl)-N-methylpyridinium iodide, or 1,1,-dilinoleyl-3,3,3′,3′-tetramethylindocarbocyanine perchloarate.

Liposomes may optionally comprise sphingolipids, in which spingosine is the structural counterpart of glycerol and one of the one fatty acids of a phosphoglyceride, or cholesterol, a major component of animal cell membranes. Liposomes may optionally contain pegylated lipids, which are lipids covalently linked to polymers of polyethylene glycol (PEG). PEGs may range in size from about 500 to about 10,000 daltons.

Liposomes may further comprise a suitable solvent. The solvent may be an organic solvent or an inorganic solvent. Suitable solvents include, but are not limited to, dimethylsulfoxide (DMSO), methylpyrrolidone, N-methylpyrrolidone, acetronitrile, alcohols, dimethylformamide, tetrahydrofuran, or combinations thereof.

Liposomes carrying the FR900359, YM-254890, or derivatives thereof, may be prepared by any known method of preparing liposomes for drug delivery, such as, for example, detailed in U.S. Pat. Nos. 4,241,046; 4,394,448; 4,529,561; 4,755,388; 4,828,837; 4,925,661; 4,954,345; 4,957,735; 5,043,164; 5,064,655; 5,077,211; and 5,264,618, the disclosures of which are hereby incorporated by reference in their entirety. For example, liposomes may be prepared by sonicating lipids in an aqueous solution, solvent injection, lipid hydration, reverse evaporation, or freeze drying by repeated freezing and thawing. In a preferred embodiment the liposomes are formed by sonication. The liposomes may be multilamellar, which have many layers like an onion, or unilamellar. The liposomes may be large or small. Continued high-shear sonication tends to form smaller unilamellar lipsomes.

As would be apparent to one of ordinary skill, all of the parameters that govern liposome formation may be varied. These parameters include, but are not limited to, temperature, pH, concentration of FR900359, YM-254890, or derivatives thereof, concentration and composition of lipid, concentration of multivalent cations, rate of mixing, presence of and concentration of solvent.

In another embodiment, a composition of the invention may be delivered to a cell as a microemulsion. Microemulsions are generally clear, thermodynamically stable solutions comprising an aqueous solution, a surfactant, and “oil.” The “oil” in this case, is the supercritical fluid phase. The surfactant rests at the oil-water interface. Any of a variety of surfactants are suitable for use in microemulsion formulations including those described herein or otherwise known in the art. The aqueous microdomains suitable for use in the invention generally will have characteristic structural dimensions from about 5 nm to about 100 nm. Aggregates of this size are poor scatterers of visible light and hence, these solutions are optically clear. As will be appreciated by a skilled artisan, microemulsions can and will have a multitude of different microscopic structures including sphere, rod, or disc shaped aggregates. In one embodiment, the structure may be micelles, which are the simplest microemulsion structures that are generally spherical or cylindrical objects. Micelles are like drops of oil in water, and reverse micelles are like drops of water in oil. In an alternative embodiment, the microemulsion structure is the lamellae. It comprises consecutive layers of water and oil separated by layers of surfactant. The “oil” of microemulsions optimally comprises phospholipids. Any of the phospholipids detailed above for liposomes are suitable for embodiments directed to microemulsions. The compound of the FR900359, YM-254890, or derivatives thereof may be encapsulated in a microemulsion by any method generally known in the art.

In yet another embodiment, the FR900359, YM-254890, or derivatives thereof, may be delivered in a dendritic macromolecule, or a dendrimer. Generally speaking, a dendrimer is a branched tree-like molecule, in which each branch is an interlinked chain of molecules that divides into two new branches (molecules) after a certain length. This branching continues until the branches (molecules) become so densely packed that the canopy forms a globe. Generally, the properties of dendrimers are determined by the functional groups at their surface. For example, hydrophilic end groups, such as carboxyl groups, would typically make a water-soluble dendrimer. Alternatively, phospholipids may be incorporated in the surface of a dendrimer to facilitate absorption across the skin. Any of the phospholipids detailed for use in liposome embodiments are suitable for use in dendrimer embodiments. Any method generally known in the art may be utilized to make dendrimers and to encapsulate compositions of the invention therein. For example, dendrimers may be produced by an iterative sequence of reaction steps, in which each additional iteration leads to a higher order dendrimer. Consequently, they have a regular, highly branched 3D structure, with nearly uniform size and shape. Furthermore, the final size of a dendrimer is typically controlled by the number of iterative steps used during synthesis. A variety of dendrimer sizes are suitable for use in the invention. Generally, the size of dendrimers may range from about 1 nm to about 100 nm.

Generally, a safe and effective amount FR900359, YM-254890, or derivatives thereof is, for example, that amount that would cause the desired therapeutic effect in a subject while minimizing undesired side effects. In various embodiments, an effective amount of an FR900359, YM-254890, or derivatives thereof described herein can substantially inhibit constitutively active G-protein signaling and treat associated diseases. In some embodiments, an effective amount is an amount capable of allosterically inhibiting the nucleotide exchange to trap constitutively active mutant Gα in the inactive GDP-bound state and as such represent a therapeutic option for treatment of diseases and disorders associated with constitutively active G-protein signaling.

When used in the treatments described herein, a therapeutically effective amount of FR900359, YM-254890, or derivatives thereof can be employed in pure form or, where such forms exist, in pharmaceutically acceptable salt form and with or without a pharmaceutically acceptable excipient. For example, the compounds of the present disclosure can be administered, at a reasonable benefit/risk ratio applicable to any medical treatment, in a sufficient amount to modulate diseases and disorders associated with constitutively active G-protein signaling.

The amount of a composition described herein that can be combined with a pharmaceutically acceptable carrier to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. It will be appreciated by those skilled in the art that the unit content of agent contained in an individual dose of each dosage form need not in itself constitute a therapeutically effective amount, as the necessary therapeutically effective amount could be reached by administration of a number of individual doses.

Toxicity and therapeutic efficacy of compositions described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals for determining the LD50 (the dose lethal to 50% of the population) and the ED50, (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index that can be expressed as the ratio LD50/ED50, where larger therapeutic indices are generally understood in the art to be optimal.

The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the disorder being treated and the severity of the disorder; activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration; the route of administration; the rate of excretion of the composition employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts (see e.g., Koda-Kimble et al. (2004) Applied Therapeutics: The Clinical Use of Drugs, Lippincott Williams & Wilkins, ISBN 0781748453; Winter (2003) Basic Clinical Pharmacokinetics, 4th ed., Lippincott Williams & Wilkins, ISBN 0781741475; Sharqel (2004) Applied Biopharmaceutics & Pharmacokinetics, McGraw-Hill/Appleton & Lange, ISBN 0071375503). For example, it is well within the skill of the art to start doses of the composition at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. If desired, the effective daily dose may be divided into multiple doses for purposes of administration. Consequently, single dose compositions may contain such amounts or submultiples thereof to make up the daily dose. It will be understood, however, that the total daily usage of the compounds and compositions of the present disclosure will be decided by an attending physician within the scope of sound medical judgment.

Again, each of the states, diseases, disorders, and conditions, described herein, as well as others, can benefit from compositions and methods described herein. Generally, treating a state, disease, disorder, or condition includes preventing or delaying the appearance of clinical symptoms in a mammal that may be afflicted with or predisposed to the state, disease, disorder, or condition but does not yet experience or display clinical or subclinical symptoms thereof. Treating can also include inhibiting the state, disease, disorder, or condition, e.g., arresting or reducing the development of the disease or at least one clinical or subclinical symptom thereof. Furthermore, treating can include relieving the disease, e.g., causing regression of the state, disease, disorder, or condition or at least one of its clinical or subclinical symptoms. A benefit to a subject to be treated can be either statistically significant or at least perceptible to the subject or to a physician.

Administration of FR900359, YM-254890, or derivatives thereof can occur as a single event or over a time course of treatment. For example, FR900359, YM-254890, or derivatives thereof can be administered daily, weekly, bi-weekly, or monthly. For treatment of acute conditions, the time course of treatment will usually be at least several days. Certain conditions could extend treatment from several days to several weeks. For example, treatment could extend over one week, two weeks, or three weeks. For more chronic conditions, treatment could extend from several weeks to several months or even a year or more.

Treatment in accord with the methods described herein can be performed prior to, concurrent with, or after conventional treatment modalities for a disease or disorder associated with constitutively active G-protein signaling.

The present disclosure encompasses pharmaceutical compositions comprising a G-protein inhibitor as disclosed above, so as to facilitate administration and promote stability of the active agent. For example, a G-protein inhibitor of this disclosure may be admixed with at least one pharmaceutically acceptable carrier or excipient resulting in a pharmaceutical composition which is capably and effectively administered (given) to a living subject, such as to a suitable subject (i.e. “a subject in need of treatment” or “a subject in need thereof”). For the purposes of the aspects and embodiments of the invention, the subject may be a human or any other animal. In particular embodiments, the subject is selected from the group consisting of primate, equine, ovine, caprine, leporine, avian, feline, rodent, or canine. Methods of preparing and administering constitutively active G-protein inhibitor disclosed herein to a subject in need thereof are well known to or are readily determined by those skilled in the art. The route of administration of a constitutively active G-protein inhibitor can be, for example, peripheral, oral, parenteral, by inhalation or topical.

(II) METHODS

The present disclosure encompasses a method of treating a disease or disorder associated with constitutively active G-protein signaling. Aberrant G-protein signaling pathways are involved in many diseases such as, in non-limiting examples, uveal melanoma, growth hormone-secreting pituitary tumors, tumors derived from Nevus of Ota, certain forms of other cancers (e.g. colon, lung, adenocarcinoma, skin melanoma, thyroid adenomas), cholera, and Sturge-Weber Syndrome. Generally, the method comprises administration of a therapeutically effective amount of FR900359, YM-254890, or derivatives thereof, so as to down-regulate constitutively active Gαsignaling, lock a G-protein in a GDP bound state, inhibit proliferation of cancer cells, re-differentiate cancer cells, increase polycomb repressive complex-2 (PRC2) activity in cancer cells, inhibit a constitutively active Ga associated disease, slow the progress of a constitutively active Ga associated disease or limit the development of a constitutively active Ga associated disease. In some embodiments the cancer cells are Uveal Melanoma (UM) cells. In another aspect, the present disclosure encompasses a method suppressing constitutively active Gαq signaling in a subject in need thereof or in a biological sample, the method comprising administering to the subject, or contacting the biological sample with a composition comprising a therapeutically effective amount of FR900359, YM-254890, derivatives thereof or combinations thereof. In yet another aspect, the present disclosure encompasses of inhibiting tumor growth in a subject in need thereof, the method comprising administering to the subject a composition comprising a therapeutically effective amount a compound FR900359, YM-254890, derivatives thereof or combinations thereof. In still yet another aspect, the present disclosure provides a composition comprising FR900359, YM-254890, derivatives thereof or combinations thereof, for use in vitro, in vivo, in situ or ex vivo. Suitable compositions comprising FR900359, YM-254890, or derivatives thereof are disclosed herein, for instance those described in Section I.

According to an aspect of the invention a pharmaceutical composition comprising FR900359, YM-254890, derivatives thereof or combinations thereof can treat, reduce, or prevent a disease, disorder, or condition associated with constitutively active Gαq signaling. As used herein the term “treating” refers to: (i) preventing a disease, disorder or condition from occurring in an animal or human that may be predisposed to the disease, disorder and/or condition but has yet been diagnosed as having it; (ii) inhibiting the disease, disorder, or condition, i.e., arresting its development or progression; and/or (iii) relieving the disease, disorder or condition, i.e., causing regression, remission of the disease, disorder and/or condition. For example, with respect to uveal melanoma, treatment may be measure by quantitatively or qualitatively to determine the presence of absence of the disease, or its progression or regression using for example symptoms associated with the diseases or clinical indication associated with the pathology.

G protein-coupled receptors (GPCRs) are integral membrane proteins that comprise one of the largest classes of proteins in the human genome. G proteins are key mediators of G protein-coupled receptor signaling, which facilitates a plethora of important physiological processes. Agonist binding to a GPCR stabilizes an active conformation of the receptor, which activates intracellular heterotrimeric guanine nucleotide binding proteins (G proteins). G proteins are composed of α, β and γ subunits, which on activation dissociate from GPCRs and modulate a range of intracellular effectors. Constitutively active G protein a subunits cause cancer, cholera, Sturge-Weber syndrome, and other disorders. Therapeutic intervention by targeted inhibition of constitutively active Gαq subunits in these disorders has yet to be achieved. Applicants have shown that constitutively active Gαq in uveal melanoma (UM) cells is inhibited by the cyclic depsipeptide FR900359 (FR), YM-254890 (YM), and derivatives thereof. Specifically, the compositions of the disclosure allosterically inhibited guanosine diphosphate—for—guanosine triphosphate (GDP/GTP) exchange to trap constitutively active Gαq in inactive, GDP-bound Gαβγ heterotrimers. Allosteric inhibition of other Gαsubunits was achieved by the introduction of an inhibitor-binding site. In UM cells driven by constitutively active Gαq, the compositions as disclosed herein inhibited second messenger signaling, arrested cell proliferation, reinstated melanocytic differentiation, and stimulated apoptosis. FR, YM and derivatives thereof promoted UM cell differentiation by reactivating polycomb repressive complex 2 (PRC2)—mediated gene silencing, a heretofore unrecognized effector system of constitutively active Gαq in UM. Constitutively active Gαq and PRC2 therefore provide therapeutic targets for diseases and disorders mediated by constitutively active Ga.

In an aspect the disclosure provides a method of re-differentiating uveal melanoma tumor cells, the method comprising contacting uveal melanoma cells with a therapeutically effective amount of FR900359, YM-254890, or derivatives thereof. As used herein, “re-differentiating” means a process by which one or more dedifferentiated cells (e.g. uveal melanoma cells) return to their original specialized form. In particular re-differentiation may include, without being limited, morphological changes indicative of re-differentiation, increased melanocytic pigmentation, and increased expression of differentiation specific gene products. In some embodiments, the disclosure provides a method of inducing polycomb repressive complex-2 mediated gene repression in uveal melanoma cells. It was surprisingly discovered that by inhibiting constitutively active Ga in uveal melanoma results in reversing the repression of gene sets that are targets of epigenetic silencing by the polycomb repressive complex 2 (PRC2), and control differentiation and development. In some embodiments, a method of re-differentiating cells includes repressing ADRA2A (alpha-adrenergic receptor-2A) and/or HAND2 (heart and neural crest derivatives expressed-2) expression or activity, comprising administering an effective amount or FR900359, YM-254890, or derivatives thereof.

In another aspect, the disclosure provides a method of locking a constitutively active guanine nucleotide-binding protein in a GDP-bound state. The method comprises administering an effective amount of FR900359, YM-254890, or derivatives thereof. In some embodiments, the method includes inhibiting downstream signaling pathways that result from constitutively active guanine nucleotide-binding proteins. In non-limiting examples, such pathways include the modulation of YAP, adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK.

In each of the above embodiments, the Gα subunit inhibitor may be selected from the group consisting of FR900359, YM-254890, a salt, prodrug or solvate thereof, an analog thereof, a derivative thereof, and any combinations thereof. The compounds according to the disclosure are effective over a wide dosage range. The exact dosage will depend upon the route of administration, the form in which the compound is administered, the subject to be treated, the body weight of the subject to be treated. Pharmaceutical compositions suitable for use in the present disclosure include compositions wherein the active ingredients are contained in a therapeutically effective amount to achieve its intended purpose. Determination of the effective amounts is well within the capability of those skilled in the art.

Depending on the specific conditions being treated, such agents may be formulated into liquid or solid dosage forms and administered systemically or locally. The agents may be delivered, for example, in a timed- or sustained- low release form as is known to those skilled in the art. Techniques for formulation and administration may be found in Remington: The Science and Practice of Pharmacy (20^(th) ed.) Lippincott, Williams & Wilkins (2000). Suitable routes may include oral, buccal, by inhalation spray, sublingual, rectal, transdermal, vaginal, transmucosal, nasal or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intra-articullar, intra-sternal, intra-synovial, intra-hepatic, intralesional, intracranial, intraperitoneal, intranasal, or intraocular injections or other modes of delivery. In a particular embodiment, the pharmaceutical composition is formulated for inhalation or oral administration.

Methods described herein are generally performed on a subject in need thereof. A subject may be a rodent, a human, a livestock animal, a companion animal, or a zoological animal. In one embodiment, the subject may be a rodent, e.g. a mouse, a rat, a guinea pig, etc. In another embodiment, the subject may be a livestock animal. Non-limiting examples of suitable livestock animals may include pigs, cows, horses, goats, sheep, llamas and alpacas. In still another embodiment, the subject may be a companion animal. Non-limiting examples of companion animals may include pets such as dogs, cats, rabbits, and birds. In yet another embodiment, the subject may be a zoological animal. As used herein, a “zoological animal” refers to an animal that may be found in a zoo. Such animals may include non-human primates, large cats, wolves, and bears. In a preferred embodiment, the subject is a human.

(III) Kits

Also provided are kits. Such kits can include an agent or composition described herein and, in certain embodiments, instructions for administration. Such kits can facilitate performance of the methods described herein. When supplied as a kit, the different components of the composition can be packaged in separate containers and admixed immediately before use. Components include, but are not limited to compositions and pharmaceutical formulations comprising a constitutively active G-protein modulation agent, as described herein. Such packaging of the components separately can, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the composition. The pack may, for example, comprise metal or plastic foil such as a blister pack. Such packaging of the components separately can also, in certain instances, permit long-term storage without losing activity of the components.

Kits may also include reagents in separate containers such as, for example, sterile water or saline to be added to a lyophilized active component packaged separately. For example, sealed glass ampules may contain a lyophilized component and in a separate ampule, sterile water, sterile saline or sterile each of which has been packaged under a neutral non-reacting gas, such as nitrogen. Ampules may consist of any suitable material, such as glass, organic polymers, such as polycarbonate, polystyrene, ceramic, metal or any other material typically employed to hold reagents. Other examples of suitable containers include bottles that may be fabricated from similar substances as ampules, and envelopes that may consist of foil-lined interiors, such as aluminum or an alloy. Other containers include test tubes, vials, flasks, bottles, syringes, and the like. Containers may have a sterile access port, such as a bottle having a stopper that can be pierced by a hypodermic injection needle. Other containers may have two compartments that are separated by a readily removable membrane that upon removal permits the components to mix. Removable membranes may be glass, plastic, rubber, and the like.

In certain embodiments, kits can be supplied with instructional materials. Instructions may be printed on paper or other substrate, and/or may be supplied as an electronic-readable medium, such as a floppy disc, mini-CD-ROM, CD-ROM, DVD-ROM, Zip disc, videotape, audio tape, and the like. Detailed instructions may not be physically associated with the kit; instead, a user may be directed to an Internet web site specified by the manufacturer or distributor of the kit.

Compositions and methods described herein utilizing molecular biology protocols can be according to a variety of standard techniques known to the art (see, e.g., Sambrook and Russel (2006) Condensed Protocols from Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, ISBN-10: 0879697717; Ausubel et al. (2002) Short Protocols in Molecular Biology, 5th ed., Current Protocols, ISBN-10: 0471250929; Sambrook and Russel (2001) Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, ISBN-10: 0879695773; Elhai, J. and Wolk, C. P. 1988. Methods in Enzymology 167, 747-754; Studier (2005) Protein Expr Purif. 41(1), 207-234; Gellissen, ed. (2005) Production of Recombinant Proteins: Novel Microbial and Eukaryotic Expression Systems, Wiley-VCH, ISBN-10: 3527310363; Baneyx (2004) Protein Expression Technologies, Taylor & Francis, ISBN-10: 0954523253).

Definitions

When introducing elements of the present disclosure or the preferred aspects(s) thereof, the articles “a,” “an,” “the,” and “said” are intended to mean that there are one or more of the elements. The terms “comprising,” “including,” and “having” are intended to be inclusive and mean that there may be additional elements other than the listed elements.

As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, and the Handbook of Chemistry and Physics, 75^(th) Ed. 1994. Additionally, general principles of organic chemistry are described in “Organic Chemistry,” Thomas Sorrell, University Science Books, Sausalito: 1999, and “March's Advanced Organic Chemistry,” 5^(th) Ed., Smith, M. B. and March, J., eds. John Wiley & Sons, New York: 2001, the entire contents of which are hereby incorporated by reference.

The term “mmol”, as used herein, is intended to mean millimole. The term “equiv”, as used herein, is intended to mean equivalent. The term “mL”, as used herein, is intended to mean milliliter. The term “g”, as used herein, is intended to mean gram. The term “kg”, as used herein, is intended to mean kilogram. The term “μg”, as used herein, is intended to mean micrograms. The term “h”, as used herein, is intended to mean hour. The term “min”, as used herein, is intended to mean minute. The term “M”, as used herein, is intended to mean molar. The term “μL”, as used herein, is intended to mean microliter. The term “μM”, as used herein, is intended to mean micromolar. The term “nM”, as used herein, is intended to mean nanomolar. The term “N”, as used herein, is intended to mean normal. The term “amu”, as used herein, is intended to mean atomic mass unit. The term “° C.”, as used herein, is intended to mean degree Celsius. The term “wt/wt”, as used herein, is intended to mean weight/weight. The term “v/v”, as used herein, is intended to mean volume/volume. The term “MS”, as used herein, is intended to mean mass spectroscopy. The term “HPLC”, as used herein, is intended to mean high performance liquid chromatograph. The term “RT”, as used herein, is intended to mean room temperature. The term “e.g.”, as used herein, is intended to mean example. The term “N/A”, as used herein, is intended to mean not tested.

As used herein, the expression “pharmaceutically acceptable salt” refers to pharmaceutically acceptable organic or inorganic salts of a compound of the invention. Preferred salts include, but are not limited, to sulfate, citrate, acetate, oxalate, chloride, bromide, iodide, nitrate, bisulfate, phosphate, acid phosphate, isonicotinate, lactate, salicylate, acid citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate, or pamoate (i.e., 1,1′-methylene-bis-(2-hydroxy-3-naphthoate)) salts. A pharmaceutically acceptable salt may involve the inclusion of another molecule such as an acetate ion, a succinate ion or other counterion. The counterion may be any organic or inorganic moiety that stabilizes the charge on the parent compound. Furthermore, a pharmaceutically acceptable salt may have more than one charged atom in its structure. Instances where multiple charged atoms are part of the pharmaceutically acceptable salt can have multiple counterions. Hence, a pharmaceutically acceptable salt can have one or more charged atoms and/or one or more counterion. As used herein, the expression “pharmaceutically acceptable solvate” refers to an association of one or more solvent molecules and a compound of the invention. Examples of solvents that form pharmaceutically acceptable solvates include, but are not limited to, water, isopropanol, ethanol, methanol, DMSO, ethyl acetate, acetic acid, and ethanolamine. As used herein, the expression “pharmaceutically acceptable hydrate” refers to a compound of the invention, or a salt thereof, that further includes a stoichiometric or non-stoichiometric amount of water bound by non-covalent intermolecular forces.

Specific embodiments disclosed herein may be further limited in the claims using “consisting of” or “consisting essentially of” language, rather than “comprising”. When used in the claims, whether as filed or added per amendment, the transition term “consisting of” excludes any element, step, or ingredient not specified in the claims. The transition term “consisting essentially of” limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristic(s). Embodiments of the invention so claimed are inherently or expressly described and enabled herein.

As various changes could be made in the above-described reporter molecules and methods without departing from the scope of the invention, it is intended that all matter contained in the above description and in the examples given below, shall be interpreted as illustrative and not in a limiting sense.

EXAMPLES

The following examples are included to demonstrate various embodiments of the present disclosure. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1: FR Traps Constitutively Active Gα in the GDP-Bound State

To determine whether constitutively active Gαq undergoes appreciable GDP/GTP exchange in UM cells a common oncogenic GTPase-defective mutant Gαq(Q209L) was evaluated for the ability to be trapped in the GDP-bound state by FR. The GDP- and GTP-bound states of Gαq(Q209L) were assessed in living cells by detecting interaction with Gβγ subunits, which bind preferentially to GDP-loaded Gαsubunits (1), or with RGS2, which binds GTP- but not GDP-loaded Gα (22). To detect protein-protein interactions, a split luciferase complementation assays was used (23), as employed to study activation state-dependent interaction between Gα subunits and cognate binding partners (24).

Results indicated that FR is able to trap constitutively active Gαq in the GDP-bound state. FR increased the level of split luciferase complementation for wild type or constitutively active Gαq interacting with Gβγ2 (FIG. 1B; EC₅₀ 3 nM and 9 nM, respectively). Conversely, FR drove constitutively active Gαq out of the active GTP-bound state, as indicated by inhibition of interaction between constitutively active Gαq and RGS2 (FIG. 1C; IC₅₀ 0.4 nM). FR was highly selective for Gαq, revealed by its lack of effect on the interaction of wild type or constitutively active Gα13 with Gβγ2 (FIG. 1A), or constitutively active Gα13 with the RGS domain of LARG (FIG. 1C). Thus, FR drives constitutively active Gαq from its active GTP-bound state into inactive GDP-bound Gαβγ complexes.

As a further test of the ability of FR to inhibit constitutively active Gαq, downstream signaling was measured. FR inhibited induction of a transcriptional reporter driven by constitutively active Gαq (FIG. 1D; IC50 1 nM), but FR had no effect on expression of the reporter when driven by constitutively active Gα13. Three amino acids involved in the FR binding site were chosen from crystallographic and mutagenesis studies using wild type Gα and an inhibitor nearly identical to FR, YM-254890 (YM) (19). Single amino-acid substitutions of each (R60K, V184S, or 1190N) in constitutively active Gαq blunted the inhibitory potency of FR (FIG. 1D; IC₅₀ 30 to 70 nM), demonstrating that FR targets constitutively active and wild type Gα by the same mechanism.

An important discovery is that GDP/GTP exchange is an underappreciated vulnerability of constitutively active G protein α-subunits, and one that can be exploited pharmacologically in UM and other diseases. Although Gα subunits undergo GDP/GTP exchange slowly in vitro, the inventors have discovered that exchange occurs in cells at rates sufficient for constitutively active Gαq to be trapped in the inactive GDP-bound state when cells are treated with FR, an allosteric inhibitor of GDP release. When trapped by FR, GDP-bound constitutively active Gαq assembles into Gαβγ heterotrimers, further suppressing GDP release and stabilizing the inactive state. Because FR-bound Gq heterotrimers are refractory to activation by GPCRs (20), signaling networks downstream of constitutively active Gαq are attenuated.

As the above work involved constitutively active Gαq in UM, it is anticipated that constitutively active forms of Gα subunit subtypes that drive other types of cancers may also be vulnerable to allosteric inhibitors of GDP release. Constitutively active Gall in UM (12) and Gα14 in vascular tumors (30) should be susceptible because wild type forms of these Gα subunits are sensitive to FR (20). Although other subtypes of Gα subunits are not sensitive to FR, all Gα subunits possess a diverged but related form of the allosteric regulatory site in Gα that binds FR. This site includes conserved features of linker 1, which stabilizes the GDP-bound state by interacting with helix 1, helix A, and helix F as part of the universal mechanism that regulates GDP release.

Example 2: FR Inhibits Gαi1 with an Engineered FR Binding Site

FR inhibits receptor-evoked signaling by wild type Gα and its close relatives Gall and Gα14, but not other Gα subunits (20). Whether FR-insensitive Gαsubunits could be converted into FR-sensitive forms by the introduction of an FR binding site was tested. It was reasoned that this might be possible because all Gαsubunits release GDP by a common allosteric mechanism (25) and because structural elements of the allosteric relay include the FR binding site (19, 25). Moreover, FR-insensitive Gα subunits do contain a similar but diverged form of the FR binding site.

To test this, eight diverged amino acids in Gαi1 to match their counterparts in the FR/YM binding site of Gαq, producing “Gαi/q” (illustrated in FIG. 2A). Gαi1 was chosen because it is insensitive to FR (20). A Gαi/q(R54K) mutant also was made, which corresponds to an amino acid substitution in Gα that blunts inhibition by YM (19). FR inhibited in vitro nucleotide exchange by Gαi/q (FIG. 2B). As expected, FR was ˜10-fold less potent toward Gαi/q(R54K). In addition, FR was able to inhibit signaling downstream of Gαi/q. FR attenuated the ability of signaling from the cannabinoid type 1 receptor via Gαi/q to inhibit forskolin-induced cAMP accumulation (IC₅₀=25 nM; FIG. 2C and FIG. 9 ). FR was ˜30-fold less potent (IC₅₀ ˜800 nM; FIG. 2C) toward Gαi/q(R54K). Thus, FR appears to inhibit Gαi/q and wild-type Gα by similar mechanisms. This finding suggests that FR-like molecules may be able to target the analogous, but distinct, binding sites of other subtypes of Gα subunits, providing a general approach to discover novel chemical probes of Gαfunction and potential therapeutics for various diseases. In addition, this approach may be efficacious for diseases that are driven by multiple GPCRs, for which blocking a single receptor is ineffective.

Example 3: FR Inhibits Signaling by Constitutively Active Gα in UM Cells

To determine whether FR inhibits signal transduction by constitutively active Gαq in UM cells, two UM cell lines (Mel202 and 92.1) driven by constitutively active Gαq(Q209L) were analyzed. A third UM cell line (OCM-1A) driven by constitutively active BRAF(V600E) served as a negative control. Signaling by Gαq-stimulated phospholipase Cβ was quantified based on levels of inositol monophosphate (IP1), a metabolically stable product of inositol 1,4,5-trisphosphate (IP3) produced by cleavage of phosphatidylinositol 4,5-bisphosphate (PIP2). In the absence of FR, IP1 levels (FIG. 3A) were >50-fold higher in Gαq(Q209L)-driven Mel202 and 92.1 cells relative to BRAF(V600E)-driven OCM-1A cells. FR reduced IP1 levels in Mel202 and 92.1 cells >50-fold (FIG. 3B), but had only modest effect (˜2-fold) on OCM-1A cells (FIG. 3B). Thus, FR strikingly inhibited second messenger production driven by constitutively active Gαq in UM cells.

Example 4: FR Inhibits UM Tumor Cell Proliferation and Survival

During the preceding experiments, it was observed that FR treatment decreased viability of Gαq(Q209L)-driven UM tumor cells. Quantification confirmed that FR inhibited proliferation of Gαq(Q209L)-driven Mel202 and 92.1 UM cells (FIG. 4A-B; EC₅₀ 6 nM and 2 nM, respectively), with no effect on proliferation of BRAF(V600E)-driven OCM-1A cells even at high concentration (10 μM). Flow cytometry revealed that FR induced cell cycle inhibition (decreased levels of S- and G2/M-phase cells) and apoptosis (increased levels of sub-G1/G0 cells) for Mel202 and 92.1 cells (FIG. 4C-D), with no effect on OCM-1A cells (FIG. 4C-D). FR therefore inhibited proliferation and survival in UM cells that had constitutively active Gαq as their oncogenic driver.

Example 5: FR Promotes Melanocytic Re-Differentiation of UM Cell Lines

FR treatment caused Gαq(Q209L)-driven Mel202 and 92.1 cells to undergo morphological changes indicative of re-differentiation. These FR-treated cells lost spindle morphology, became flatter, and produced multiple projections (FIG. 5A), when compared with vehicle-treated cells or FR-treated OCM-1A cells. FR strikingly increased melanocytic pigmentation in Mel202 and 92.1 cells, compared with vehicle-treated cells or FR-treated OCM-1A cells (FIG. 5B). FR increased the expression levels of two pigmentation enzymes (tyrosinase (TYR) and dopachrome tautomerase (DCT)) and a melanosome structural protein (PMEL) in Mel202 and 92.1 cells but not in OCM-1A cells (FIG. 5C). Thus, FR antagonized the de-differentiation process driven by constitutively active Gαq in UM cells.

To explore how FR regulates UM cell phenotypes, global gene expression by RNA-Seq was performed. First, the inventors focused on YAP-regulated genes because the YAP protein is activated downstream of constitutively active Gαq in UM cell lines (26, 27). As expected, certain YAP target genes were downregulated by FR; however, others were upregulated (FIG. 6A). Moreover, FR caused increases in the expression of a YAP-driven transcriptional reporter in Mel202 and 92.1 cells (EC50 0.8 and 3 nM, respectively; FIG. 6B), but FR had no effect in BRAF(V600E)-driven OCM-1A cells (FIG. 6B). Therefore, rather than simply activating YAP to induce target gene expression, constitutively active Gαq exerts gene-specific effects on YAP-mediated transcription.

FR caused an apoptotic response in UM cells, as described above. However, FR treatment did not lead to striking upregulation of pro-apoptotic genes or to downregulation of survival genes. Instead, two pro-apoptotic members of the BCL2 family were downregulated modestly in response to FR— BBC3/PUMA decreased 3.5-fold (p<0.001) and PMAIP1/NOXA decreased 2.5-fold (p<0.001) (FIG. 9 ). No other BCL2 family members showed significant change (p<0.05, fold change >2), and broader examination of apoptosis-related genes showed only small effects (FIG. 9 ). These results are consistent with evidence that intrinsic and extrinsic apoptotic pathways function independently of gene transcription (28, 29).

Cell-cycle genes were also relatively unaffected by FR, as indicated by gene set enrichment analysis and direct comparison of the RNA-Seq data (FIG. 9 and Table 1). The cyclin-dependent kinase inhibitor p21CIP1 (CDKN1A, down 3.0 fold, p<0.001) was downregulated, and several cell cycle genes showed upward trends lacking statistical significance (p>0.05, fold change <2) (FIG. 9 ). Targets of E2F, a transcription factor positively regulated by cyclin-dependent kinases, were positively enriched (Table 1). These results suggest that the anti-proliferative effects of FR are not mediated primarily by short-term changes in cell cycle gene expression.

TABLE 1 Gene Set Enrichment Positive Correlation NOM

FWER RANK NAME SIZE ES NES p-val q-val p-val AT MAX DUTERIRE_ESTRADIOL_RESPONSE_24HR_UP 264 0.6517718 3.44795 0 0 0 1877 XOBAYASHI_EGFR_SIGNALING_24HR_ON

0

0.662429 3.421171 0 0 0 2070 ZHANG_TIX_TARGETS_60HR_ON 230 0.64

2758 3.392733 0 0 0 20

0

OSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER 120 0.7079712 3.349099 0 0 0 1252 FOURNIER_A

NAR_DEVELOPMENT_LATE_2 222 0.6335315 3.348332 0 0 0 2283 SOTHRIOU_BREAST_CANCER_GRADE_1_VS_3_UP 124 0.

922286 3.341391 0 0 0 1433 WINNEPENNINCKK_MELANOMA_METASTASIS_UP 128 0.6813596 3.2

8367 0 0 0 1248 KROONQUIST_IL

_DEPRIVATION_UN 81 0.7235784 3.209366 0 0 0 1761 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP 10

0.67

3432 3.206096 0 0 0 2326 MITSIAGES_RESPONSE_TO_APLIOIN_DN 210 0.622916 3.205297 0 0 0 2103 PENG_LEUCINE_DEPRIVATION_DN 152 0.6417515 3.204675 0 0 0 2063 SHEDOIN_LUNG_CANCER_POOR_SURVIVAL_A

338 0.5789082 3.164519 0 0 0 2483 ZHANG_T

X_TARGETS_DN 77 0.7067005 3.159272 0 0 0 20

0 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP 4

0 0.5668274 3.154917 0 0 0 2244 CHANG_CYCLING_GENES 119 0.6553933

.149018 0 0 0 1980

ANG_DOXORUBICIN_RESISTANCE_UP 50 0.7535572 3.106621 0 0 0 1423

EN_INTESTINE_PROBIOTICS_24HR_UP 387 0.

622881 3.10513

0 0 0 2857 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP 1

4 0.6312098 3.090752 0 0 0 2243 WHITEFORD_PEDIATRIC_CANCER_MARKERS 94 0.6717131 3.080914 0 0 0 1423 PU

ANA_BBCA2_PCC_NETWORK 294 0.57710908 3.0742

8 0 0 0 20

MARSON_BOUND_BY_E2F4_UNSTIMULATED 459 0.5462862 3.072465 0 0 0 2244 BASAM_V

K1_TARGETS_UP 205 0.5920223 3.06783 0 0 0 1873 BLUM_RESPONSE_TO_SAURASIB_DN 265 0.5754255 3.063616 0 0 0 2066 ZHANG_TLX_TARGETS_36HR_DN 143 0.5208622 3.060966 0 0 0 2108 REACTOME_CELL_CYCLE_MITOTIC 222 0.

800772 3.036345 0 0 0 2316 BURTON_ADIPOGENESIS_3 84 0.

783643 3.031054 0 0 0 2050 FU

_VBX1_TARGETS_DN 155 0.

078871 3.02593 0 0 0 2541 ODONNELL_TFRC_TARGETS_DN

0 0.6

65859 3.017551 0 0 0 1976 C

OONQUIST_NRAS_SIGNALING_DN 63 0.7114243 3.016316 0 0 0 1243 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP 1

3 0.6183688 3.014

3 0 0 0 2263 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR 99 0.6436814 3.009894 0 0 0 2244

_METASTASIS_UP 159 0.5994755 2.989941 0 0 0 2283 HOFFMANN_LARGE_TO_SMALL_PRE_B

_LYMPHOCYTE_UP 128 0.6149781 2.98444 0 0 0 2244 ZHAN_MULTIPLE_MYELOMA_PR_UP 40 0.75

0601 2.97705

0 0 0 1980 HORUICHI_WTAP_TARGETS_DN 224 0.568034

2.

70475 0 0 0 2408 LEE_EARLY_T_LYMPHOCYTE_UP 78 0.6722333 2.966888 0 0 0 1423 PENG_GLUTAMINE_DEPRIVATION_DN 243 0.5665463 2.9

5871 0 0 0 1986 REACTOME_DNA_REPLICATION 140 0.6076682 2.961261 0 0 0 1989 REACTOME_MITOTIC_M_M_GI_PHASES 122 0.6165375 2.96116

0 0 0 2050 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN 72 0.6737723 2.959949 0 0 0 2017 MORI_IMMATURE_B_LYMPHOCYTE_DN 76 0.660201

2.

47281 0 0 0 2

FURUKAWA_DUSP6_TARGETS_

_DN 48 0.742

728 2.93713 0 0 0 1333 MORI_LARGE_PRE_B

_LYMPHOCYTE_UP 71 0.6629807 2.92042

0 0 0 1783 KAUFFMANN_MELANOMA_RELAPSE_UP 48 0.7180015 2.918148 0 0 0 1754

_E2F_TARGETS 47 0.727009

2.9137

1 0 0 0 2244 CHIANG_LIVER_CANCER_SUBLCASS_PROLIFERATION_UP 129 0.5999274 2.910144 0 0 0 2041 MANALO_HYPOXIA_DN 228 0.5593274 2.909117 0 0 0 2879 LINDGREN_BLADDER_CANCER_CLUSTER_3_UP 215 0.5544321 2.904898 0 0 0 2885 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR 71 0.6622609 2.8

3702 0 0 0 2244 BERENIENO_TRANSFORMED_BY_RHOA_UP 377 0.5261049 2.876792 0 0 0 2246 ODONNELL_TARGETS_OF_MYC_ANG_TFRC_DN 37 0.7402481 2.872902 0 0 0 1976 XONG_E2F3_TARGETS 29 0.640658 2.84977

0 0 0 1980 PUIANA_XPRS5_INT_NETWORK 128 0.5951415 2.847488 0 0 0 2332 WANG_RESPONSE_TO_GSK3_IN

TOR_S

21

763_DN 240 0.5399863 2.844691 0 0 0 1963 REACTOME_CELL_CYCLE 2

0.5292531 2.83

72 0 0 0 2316 TATE_PLASMA_CELL_VS_PLASMABLAST_DN 222 0.5382779 2.815545 0 0 0 2194 GACIN_FOXP3_TARGETS_CLUSTER_P

5

0.884676 2.804849 0 0 0 1939 HENPORATH_PROLIFERATION 102 0.6039323 2.802778 0 0 0 1980 M

LENAAR_TARGETS_OF_CCND1_AND_CDKA_DN 45 0.6947311 2.793475 0 0 0 1899 WHITFIELD_CELL_CYCLE_G2_M 142 0.5631633 2.788675 0 0 0 2494 YU_MYC_TARGETS_UP 34 0.7430208 2.767473 0 0 0 1737 PUIANA_BRCA_CENTERED_NETWORK 94 0.6085714 2.765684 0 0 0 2050 MARKEY_RB1_ACUTE_LOF_UP 169 0.

481748 2.748592 0 0 0 2

36 QU_APOPTOSIS_BY_CDKN1A_VIA_TP53 49 0.6737988 2.7449 0 0 0 1813 BENPORAIM_CYCLING_GENES 430 0.4913681 2.744477 0 0 0 2244 PUIANA_BREAST_CANCER_WITH_BRCA

_MUTATED_UP 46 0.6713083 2.7302

0 0 0 2308 MISSIAG

A_REGULATED_BY_METHYLATION_DN 98 0.589051

2.728933 0 0 0 2244 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN 43 0.684554

2.725551 0 0 0 1147 VANTVEER_BREAST_CANCER_METASTASIS_DN 84 0.5959497 2.710735 0 0 0 2244

2F_Q4 162 0.5403296 2.708875 0 0 0 2332 LINDGREN_BLADDER_CANCER_CLUSTER_1_DN 237 0.52073 2.702628 0 0 0 2714 TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C 302 0.4

61034 2.70057 0 0 0 2893

AMMINGA_

2_TARGETS 33 0.7312832 2.699502 0 0 0 1783 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN 463 0.4778171 2.696775 0 0 0 2897

EN_BOUND_BY_E2F 52 0.6574689 2.69413

0 0 0 2383 STEIN_

_TARGETS_RESPONSIVE_TO_ESTROGEN_DN 31 0.7390018 2.688479 0 0 0 1525 E2F_Q5 162 0.5322467 2.679208 0 0 0 2332

_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN 125 0.550080

2.67384

0 0 0 2399 SONG_TARGETS_OF_IE85_CMV_PROTEIN 52 0.6557211 2.667125 0 0 0 1055 MOHANKUMAH_TLX1_TARGETS_UP 274 0.5005348 2.661168 0 0 0 2589 AMUNDSON_GAMMA_RADIATION_RESPONSE 34 0.7198703 2.650388 0 0 0 1243 WEST_ADRENOCORTICAL_TUMOR_UP 222 0.5045997 2.648262 0 0 0 2714 REACTOME_MITOTIC_PROMETAPHASE 66 0.6150

4 2.64642 0 0 0 1989 KAUFFMANN_DNA_REPLICATION_GENES 300 0.5681802 2.6462 0 0 0 2050 BURTON_ADIPOGENESIS_PEAK_AT_16

2 0.7150328 2.

440

0 0 0 2190 WHITFIELD_CELL_CYCLE_LITERATURE 42 0.6811483 2.642025 0 0 0 1762 PUIANA_BREAST_CANCER_LIT_INT_NETWORK 73 0.5915995 2.639938 0 0 0 1768

CHI_CELL_CYCLE_RB1_TARGETS 21 0.8039092 2.637239 0 0 0 1248 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP 65 0.6206203 2.637116 0 0 0 1731 GOLDRATH_ANTIGEN_RESPONSE 216 0.5083296 2.

36951 0 0 0 2219 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 191 0.5185849 2.632348 0 0 0 2390

_TNC_TARGETS_DN 109 0.5581724 2.629792 0 0 0 1482 CSR_LATE_UP

_UP 118 0.5494

02 2.629753 0 0 0

042 RODRIGUES_THYROID_CARCINOMA_POORLY_DIF- 462 0.4635281 2.627287 0 0 0 3092 FERENTIATION_UP TANG_SENESCENCE_TP53_TARGETS_DN 46 0.6643747 2.626405 0 0 0 1229 REACTOME_MITOTIC_G1_G1_

_PHASES 90 0.5750307 2.625195 0 0 0 2640 LE_EGR2_TARGETS_UP 86 0.588038 2.625156 0 0 0 1810 CHEMNIT2_RESPONSE_TO_PROSTAGLANDIN_E2_UP 102 0.5599114 2.623393 0 0 0 1737 VECCHI_GASTRIC_CANCER_EARLY_UP 273 0.4884897 2.618871 0 0 0 2757 E2F4DP1_

2 158 0.5221322 2.61598 0 0 0 2219 REACTOME_G2_M_CHECKPOINTS 35 0.

854786 2.613967 0 0 0 1754 REACTOME_DNA_STRAND_ELONGATION 26 0.7390443 2.613621 0 0 0 1063 AFFAR_YY1_TARGETS_DN 141 0.5318596 2.609855 0 0 0 1529 FARMER_BREAST_CANCER_CLUSTER_2 2

0.7388588 2.606811 0 0 0 1390 E2F_

2 157 0.5222832 2.603409 0 0 0 2219

ORC

_MALIGNANT_MESOTHELIOMA_UP 217 0.499816 2.593

73 0 0 0 2957 REACTOME_ACTIVATION_OF_THE_PRE_REP- 23 0.7647482 2.593947 0 0 0 926 LICATE_COMPLEX PID_AURORA_B_PATHWAY 29 0.7211104 2.592803 0 0 0 2219 TGASTMAGC_NFE2_

1 114 0.5554186 2.592271 0 0 0 2332 E2F4

P2_

1 157 0.5171896 2.59170

0 0 0 2219 E2F1_Q6 1

8 0.5178887 2.591212 0 0 0 2219 POOLA_INVASIVE_BREAST_CANCER_UP 116 0.54061 2.589162 0 0 0 1737 E2F0

P2_

1 157 0.5171496 2.585

3 0 0 0 2219 E2F1

PIRB_D1 153 0.5126388 2.57999 0 0 0 2332 BOYAULT_LIVER_CANCER_SUBLCLASS_

3_UP 141 0.5222583 2.579289 0 0 0 3136 REACTOME_CELL_CYCLE_CHECKPOINTS 78 0.565227 2.569227 0 0 0 2640 REACTOME_

_PHASE 74 0.5798341 2.567453 0 0 0 2050 REACTOME_G1_

_TRANSITION 72 0.5878485 2.5533

0 0 0 2640 KEGG_CELL_CYCLE 93 0.5568015 2.551866 0 0 0 1539 E2F1DP1_

157 0.517149

2.550628 0 0 0 2219 REACTOME_SYNTHESIS_OF_DNA 63 0.5880677 2.548754 0 0 0 2050 SUNG_METASTASIS_STROMA_DN 33 0.

897342 2.543812 0 0 0 1818 MUELLER_PLURINET 18

0.4952148 2.543881 0 0 0 2778 REACTOME_M_G1_TRANSITION 52 0.62

9346 2.541686 0 0 0 2640

_ERYTHROID_DIFFERENTIATION 53 0.6260986 2.541519 0 0 0 2174 ERRERT_PROGENITOR 91 0.548630

2.532053 0 0 0 2394 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 165 0.5020148 2.529642 0 0 0 2222 BURTON_ADIPOGENESIS_AT_24HR 34 0.6768

6 2.529516 0 0 0 140

VEGF_A_UP.V1_DN 134 0.5142433 2.523708 0 0 0 3110 GAL_LEUKEMIC_STEM_CELL_DN 105 0.5435259 2.521694 0 0 0 1939 LY_AGING_OLD_DN 41 0.656711 2.51529 0 0 0 22

SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN 17 0.8156967 2.514904 0 0 0 1243 REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION 50 0.6125944 2.497355 0 0 0

416 REICHERT_MITOSIS_

_TARGETS 24 0.727967 2.496264 0 0 0 2173 ELVIDGE_HYPOXIA_DN 104 0.5344598 2.492277 0 0 0 2483 REACTOME_ACTIVATION_OF_ATR_IN_RE- 29 0.6882426 2.491589 0 0 0 1754 SPONSE_TO_REPLICATION_STRESS CHANG_CORE_SERUM_RESPONSE_UP 144 0.5119669 1.490964 0 0 0 3046 REACTOME_PROCESSING_OF_CAPPED_INTRON_CON- 94 0.5461728 2.490088 0 0 0 1894 TAINING_PRE_MRNA E2F1_Q3 155 0.4989949 2.489905 0 0 0 2219 E2F_01 44 0.62

5794 2.489184 0 0 0 156

ADER

_BREAST_CANCER_PROGNOSIS_UP 29 0.6738477 2.486231 0 0 0 1873 ZHENG_GLIOBLASTOMA_PLASTICITY_UP 168 0.4924908 2.47083 0 0 0 1873 PENG_RAPAMYCIN_RESPONSE_DN 177 0.4896024 2.464535 0 0 0 2766 REACTOME_MITOTIC_G2_G2_M_PHASES 56 0.5

10709 2.456503 0 0 0 2281

HATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP 73 0.5654142 2.454489 0 0 0 2347 E2F1_UP.V1_UP 127 0.5119882 2.452826 0 0 0 2553 GARY_CDS_TARGETS_DN 279 0.4585115 2.452447 0 0 0 3160 BURTON_ADIPOGENESIS_2 51 0.5927104 2.447

49 0 0 0 171

MORE_PRE_BI_LYMPHOCYTE_UP 57 0.5828884 2.446

45 0 0 0 1781 II_RESPONSE_TO_FSH_DN 43 0.6178514 2.425181 0 0 0 2381 KAUFFMANN_DNA_REPAIR_GENES 157 0.4887121 2.433041 0 0 0 3019 CAIRO_HEPATOBLASTOMA_CLASSES_UP 423 0.4375872 2.428374 0 0 0 2244 E2F_Q4_01 147 0.4877

7 2.411003 0 0 0 2332 E2F_03 160 0.4781991 2.388575 0 0 0 2332 GCNP_SHH_UP_LATE, V1_UP 116 0.49

4835 2.354005 0 0 0 2533 E2F_Q6_01 152 0.4698

52 2.330773 0 0 0 2332 E2F_Q3 140 0.471848

2.327572 0 0 0 2332 E2F_Q3_01 148 0.4733464 2.315264 0 0 0 2072 E2F1_Q4_01 142 0.4668199 2.309434 0 0 0 2072 E2F1_Q

_01 159 0.4528135 2.271717 0 0 0 2215 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHO- 34 0.6431882 2.381599 0 6.94E−06 0.001 1965 LIPIDS_TURQUOISE_DN GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP 53 0.5729079 2.385526 0 6.99E−06 0.001 1737 SU_TESTIS 4

0.6052453 2.38601 0 7.03E−06 0.001 2583 PATIL_LIVER_CANCER 491 0.4270232 2.389805 0 7.08E−06 0.001 2894 VERNELL_RETINOBLASTOME_PATHWAY_UP 62 0.5558563 2.390936 0 7.13E−06 0.001 2017 WONG_EMBRYONIC_STEM_CELL_CORE 237 0.4531235 2.394108 0 7.18E−06 0.001 1848 KEGG_DNA_REPLICATION 27 0.6996688 2.396272 0 7.23E−06 0.001 1754 MORE_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP 65 0.5518671 2.3

72 0 7.28E−06 0.001 2879 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION 49 0.5913903 2.401491 0 7.33E−06 0.001 1553 OSMAN_BLADDER_CANCER_UP 255 0.4531255 2.404237 0 7.38E−06 0.001 2631 PIO_P

_PATHWAY 36 0.

2

8197 2.407149 0 7.44E−06 0.001 1243 WILCOX_RESPONSE_TO_PROGESTERONE_UP 96 0.52410

5 2.413156 0 7.49E−06 0.001 1762 KEGG_OOCYTE_MEIOSIS 63 0.5720019 2.414789 0 7.54E−06 0.001 2610 LI_WILMS_TUMOR_ANAPLASTIC_UP 18 0.7413288 2.351513 0 1.34E−05 0.002 1223 WHITFIELD_CELL_CYCLE_G2 119 0.4957932 2.357127 0 1.35E−05 0.002 1456 MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP 257 0.4436246 2.357686 0 1.36E−05 0.002 3483

_BREAST_CANCER_RINOME_

1

0.7686798 2.3583 0 1.36E−05 0.002 2243 REACTOME_MRNA_PROCESSING 107 0.500

405 2.364086 0 1.37E−05 0.002 1981 REACTOME_TRANSPORT_OF_MATURE_TRAN- 39 0.6155682 2.364106 0 1.38E−05 0.002 1848 SCRIPT_TO_CYTOPLASM FEVR_CTNNB1_TARGETS_DN 368 0.4308235 2.378087 0 1.39E−05 0.002 2573

OYAULT_LIVER_CANCER_SUBCLASS_G23_UP 40 0.6095077 2.347648 0 2.00E−05 0.003 1038 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP 492 0.4135969 2.309747 0 2.50E−05 0.004 2647 RHODES_UNDIFFERENTIATED_CANCER 50 0.5741092 2.312351 0 2.52E−05 0.004 1771 STEIN_ESR1_TARGETS 57 0.5478188 2.320627 0 2.53E−05 0.004 1525 PID_ATR_PATHWAY 34 0.6201547 2.

28239 0 2.55E−05 0.004 1768 REACTOME_ASSEMBLY_OF_THE_PRE_REP- 42 0.5948156 2.328291 0 2.56E−05 0.004 2640 LICATIVE_COMPLEX

OCARTA_MCM_PATHWAY 1

0.7687059 2.331338 0 2.58E−05 0.004 256 REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUB- 25 0.6869984 2.531537 0 2.59E−05 0.004 1495 SEQUENT_MODIFICATION BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP 33 0.6305398 2.33323 0 2.61E−05 0.004 3070 PID_

DC42_PATHWAY 50 0.5685199 2.53457 0 2.63E−05 0.004 2769 ZHANG_BREAST_CANCER_PROGENITORS_UP 279 0.438684 2.34155 0 2.64E−05 0.004 2426 WHITFIELD_CELL_CYCLE_G1_

96 0.5123215 2.341555 0 2.

6E−05 0.004 2877 REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIM- 51 0.5613973 2.297269 0 3.07E−05 0.005 3136 UATED_GENES REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE 48 0.5779655 2.298501 0 3.09E−05 0.005 2627 PAL_PRMTS_TARGETS_UP 124 0.480239 2.299389 0 3.10E−05 0.005 2571 ENK_UV_RESPONSE_KERATINOCYTE_DN 328 0.4257683 2.291295 0 3.61E−05 0.006 3038 GEORGES_CELL_CYCLE_MIR192_TARGETS 49 0.5611235 2.29236 0 3.63E−05 0.006 2001 VANIVEER_BREAST_CANCER_ESR1_DN 151 0.4659884 2.294941 0 3.65E−05 0.006 1732 REACTOME_MNC_CLASS_II_ANTIGEN_PRESENTATION 61 0.5386897 2.271817 0 4.08E−05 0.007 2329 REACTOME_G1_S_SPECIFIC_TRANSCRIPTION 15 0.758102 2.273017 0 4.10E−05 0.007 857 FAELT_B_CLL_WITH_VH3_21_UP 35 0.6047155 2.275127 0 4.13E−05 0.007 2362 PID_FOXM1_PATHWAY 30 0.6251206 2.275983 0 4.15E−05 0.007 1525 REACTOME_KINESINS 18 0.7059842 2.280051 0 4.17E−05 0.007 736 REACTOME_MRNA_SPLICING 71 0.5256779 2.289946 0 4.20E−05 0.007 1894 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN 332 0.413126 2.258007 0 4.63E−05 0.008 3146 IGCACTI_MIR519C_MIR

B_MIR519A 266 0.4066616 2.1657 0 5.11E−05 0.001 2292 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP 125 0.470616 2.261943 0 5.14E−05 0.009 2931 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP 81 0.5071876 2.262118 0 5.17E−05 0.009 2737

_EZH2_TARGETS_DN 217 0.4301757 2.236008 0 5.82E−05 0.001 2126 REACTOME_RECRUITMENT_OF_MITOTIC_CENTRO- 45 0.559968 2.240593 0 5.85E−05 0.011 2281 SOME_PROTEINS_AND_COMPLEXES A

AMSON_INTERACT_WITH_AIR

38 0.5720327 2.241129 0 5.88E−05 0.011 1886 REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES 41 0.5645759 2.241887 0 5.91E−05 0.011 2281 HOLLMANN_APOPTOSIS_VIA_CD40_UP 129 0.4596237 2.24277 0 5.94E−05 0.011 1817 REACTOME_FORMATION_OF_TU

_FOLDING_INTER- 17 0.7198963 2.247552 0 5.97E−05 0.011 2626 MEDIATES_BY_CCT_

CHARAF

_BREAST_CANCER_LUMINAL_VS_ME- 304 0.4141847 2.24982 0 6.00E−05 0.011 2233 SENCHYMAL_DN WELSCH_BRCA1_TARGETS_DN 109 0.4807689 2.249974 0 6.03E−05 0.011 1984 ALCALAY_AML_BY_NPM1_LOCALIZATION_DN 117 0.4726266 2.26075 0 6.06E−05 0.011 1762 WHITFIELD_CELL_CYCLE_5 101 0.4808036 2.252008 0 6.09E−05 0.011 2050 RMEIN_GLUCOCORTICOID_THERAPY_DN 234 0.4290472 2.252641 0 6.13E−05 0.011 2786 CHICAS_RB1_TARGETS_SENESCENT 338 0.4124367 2.253956 0 6.16E−05 0.011 1980

_E2F3_ONCOGENIC_SIGNATURE 1

1 0.4473504 2.256184 0 6.19E−05 0.011 2498 REACTOME_E2F_MEDIATED_REG- 25 0.5585140 2.256432 0 6.23E−05 0.011 1245 ULATION_OF_DNA_REPLICATION SASSON_RESPONSE_TO_GONADOTRPHINS_UP 58 0.5308755 2.229892 0 6.31E−05 0.012 1766 SENESE_HDAC1_TARGETS_UP 277 0.4140907 2.222115 0 7.26E−05 0.014 3208

_PSEUDOPODIA_HAPTOTAXIS_DN 438 0.395995 2.22225 0 7.30E−05 0.014 3049 ONDER_CDH1_TARGETS_1_DN 89 0.4845379 2.224719 0 7.22E−05 0.014 1741 SASAKI_ADULT_T_CELL_LEUKEMIA 113 0.4693115 2.213253 0 7.73E−05 0.015 3371 SCHMIDT_FOR_TARGETS_IN_LIMB_BUD_UP 20 0.6919208 2.231637 0 8.16E−05 0.016 1870 PID_PDGFRB_PATHWAY 88 0.4862162 2.232389 0 8.20E−05 0.016 2261 REACTOM_GLUCONE_TRANSPORT 26 0.6342709 2.21081 0 8.64E−05 0.017 1848 TBK1DF_DN 185 0.4340437 2.200987 0 1.01E−04 0.001 2610 mARTORIATE_MDM4_TARGETS_FETAL_LIVER_DN 321 0.4046304 2.198309 0 1.16E−04 0.023 3220

_OVARIAN_CANCER_INVAVSIVE_VS_LMP_UP 82 0.4908294 2.190942 0 1.20E−04 0.024 2167 ELVIDGE_HIF1A_TARGETS_UP 47 0.5452291 2.195089 0 1.20E−04 0.024 3177 RB_P107_0N, L1_UP 82 0.4941093 2.215586 0 1.21E−04 0.001 1899 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN 15 0.7217879 2.197403 0 1.21E−04 0.024 1218 KEGG_CITRATE_CYCLE_TCA_CYCLE 23 0.649862 2.188362 0 1.23E−04 0.025 1825 REACTOME_B

_INFECTION 117 0.4638732 2.188439 0 1.24E−04 0.025 2512 REACTOME_TRANSPORT_OF_MATURE_MRNA_DE- 25 0.6257544 2.187429 0 1.28E−04 0.026 1848 RIVED_FROM_AN_INTRONLESS_TRANSCRIPT MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN 173 0.4324481 2.183882 0 1.30E−04 0.027 3565 PIO_TCR_PATHWAY 30 0.600023 2.184291 0 1.31E−04 0.027 2335 PIO_AURORA_A_PATHWAY 22 0.6657441 2.185917 0 1.31E−04 0.027 2674 REACTOME_APC_C_CDH1_MEDIATED_DEGRADA- 38 0.5599772 2.186917 0 1.32E−04 0.027 2627 TION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_(—) PROTEINS_IN_LATE_MITOSIS_EARLY_G1 BASSO_

_LYMPHOCYTE_NETWORK 91 0.4691338 2.175064 0 1.33E−04 0.028 1434 SENESE_HDAC2_TARGETS_UP 69 0.4932556 2.178892 0 1.33E−04 0.028 2516 GROSS_HYPOXIA_VIA_ELK3_UP 136 0.44319 2.178925 0 1.34E−04 0.028 2219 DOUGLAS_

_TARGETS_UP 360 0.396865 2.179383 0 1.34E−04 0.028 1909 REACTOME_NEP_NS2_INTERACTS_WITH_THE_CEL- 21 0.6471572 2.1

343 0 1.39E−04 0.03 1848 LULAR_EXPORT_MACHINERY KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION 35 0.5693248 2.166747 0 1.40E−04 0.03 1552 JIANG_VHL_TARGETS 80 0.4892545 2.171472 0 1.40E−04 0.03 2499 PIC_E2F_PATHWAY 58 0.52042 2.171815 0 1.41E−04 0.03 875 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN 55 0.5186248 2.174135 0 1.41E−04 0.03 1959 KEGG_FC_GAMMA_

_MEIATED_PHAGOCYTOSIS 56 0.5262478 2.153769 0 1.43E−04 0.031 2529

ENPORAIN_17513976.21_2 23 0.5457991 2.16050

0 1.47E−04 0.032 1887 PRAMOONIAGO_SOX4_TARGETS_DN 38 0.5652034 2.15772 0 1.51E−04 0.033 2102 REACTOME_DOUBLE_STRAND_BREAK_REPAIR 18 0.68211 2.155988 0 1.64E−04 0.036 1768 IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR 264 0.4037208 2.155303 0 1.68E−04 0.037 3071 GARCIA_TARGETS_OF_FL

_AND_DAX1_DN 163 0.4627588 2.152591 0 1.80E−04 0.04 1939 BIOCARTA_RHO_PATHWAY 25 0.6245347 2.153595 0 1.81E−04 0.04 2377 REACTOME_FACTORS_INVOLVED_IN_MEGAKAR- 65 0.4943024 2.34644 0 1.92E−04 0.043 2615 YOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION WHITFIELD_CELL_CYCLE_M_G2 89 0.474211 2.151257 0 1.92E−04 0.043 3022 REACTOME_METABOLISM_OF_NON_CODING_RNA 32 0.5724509 2.141542 0 2.03E−04 0.046 1848 SHIPP_D

CL_VS_FOLLICULAR_LYMPHOMA_UP

0.57229

3 2.142214 0 2.03E−04 0.046 2175 REACTOME_APC_C_CDC20_MEDIATED_DEGRADA- 39 0.5517606 2.142244 0 2.04E−04 0.046 2627 TION_ OF_MITOTIC_PROTEINS REACTOME_CHOLESTEROL_BIOSYNTHESIS 18 0.6780912 2.138251 0 2.09E−04 0.048 221

_ESTRADIOL_RESPONSE_6HR_UP 163 0.4279309 2.13847 0 2.10E−04 0.048 1427 REACTOME_HOST_INTERACTIONS_HIV_FACTORS 73 0.4871194 2.139001 0 2.10E−04 0.048 2443

_APOPTOSIS_BY_REOVIRUS_INFECTION_DN 211 0.4087728 2.136984 0 2.12E−04 0.049 2093 SMIRNOV_RESPONSE_TO_IR_6HR_DN 72 0.4874165 2.135013 0 2.16E−04 0.05 2310 WAKASUGI_HAVE_ZNF143_BINDING_SITES 40 0.5463916 2.134691 0 2.18E−04 0.051 1085 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN 446 0.3819454 2.134862 0 2.19E−04 0.051 3027 #CAFFAREL_RESPONSE_TO_THC_DN 24 0.6253232 2.134149 0 2.21E−04 0.052 1473

_

1 134 0.4368284 2.127377 0 2.26E−04 0.005 2122 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN 27 0.5871342 2.132109 0 2.32E−04 0.053 1437 JOHNSTONE_PARVES_TARGETS_2_DN 206 0.4127925 2.132638 0 2.33E−04 0.053 2470 SP1_Q4_01 135 0.4345556 2.133049 0 2.37E−04 0.005 2258 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN 119 0.4435938 2.129865 0 2.42E−04 0.056 3818 REACTOME_ADAPTIVE_IMMUNE_SYSTEM 279 0.3978644 2.130015 0 2.43E−04 0.056 2360 PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP 61 0.5104208 2.126163 0 2.66E−04 0.062 2244

_HYPOXIA_NOT_VIA_

459 0.3777474 2.124628 0 2.68E−04 0.063 2684 SHEPARD_BMYB_TARGETS

1 0.5122973 2.124899 0 2.69E−04 0.063 1423 PODAR_RESPONSE_TO_ADAPHOSTIN_DN 16 0.6921382 2.116942 0 3.07E−04 0.071 864 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP15 29 0.5858846 2.116321 0 3.13E−04 0.073 2137 REACTOME_G0_AND_EARLY_G1 18 0.5589424 2.109192 0 3.49E−04 0.082 2610 SCIBETTA_KDMS8_TARGETS_DN 56 0.4985609 2.107092 0 3.59E−04 0.085 3054 REACTOME_

_REMOVAL_FROM_CHROMATIN 42 0.5346347 2.104473 0 3.70E−04 0.087 2640 LY_AGING_PREMATURE_DN 23 0.62672 2.102505 0 3.77E−04 0.089 2233 PIC_FCER1_PATHWAY 33 0.5656276 2.101537 0 3.83E−04 0.091 2529 CSR_EARLY_UP.V1_UP 97 0.4600552 2.136143 0 3.85E−04 0.004 3200 REACTOME_DNA_REPAIR 68 0.4835479 2.100369 0 3.85E−04 0.092 1886 PIC_FANCONE_PATHWAY 35 0.5660556 2.096959 0 3.92E−04 0.094 2089 BENPORATH_ES_1 240 0.399723 2.092987 0 4.10E−04 0.098 2778 NPS14_DN.V1_DN 120 0.4491469 2.132656 0 4.20E−04 0.005 1939 LINSLEY_MIR16_TARGETS 129 0.4327073 2.091803 0 4.20E−04 0.101 3168 WINTER_HYPOXIA_UP 56 0.5079345 2.091212 0 4.23E−04 0.102 2586

_

_Q6 419 0.3720492 2.070286 0 4.30E−04 0.01 2521 OXFORD_RALA_OR_RALB_TARGETS_UP 39 0.5439909 2.088946 0 4.37E−04 0.106 1053 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUG- 26 0.5975822 2.087967 0 4.43E−04 0.108 2238 AR_METABOLISM SASSON_RESPONSE_TO_FORSKOLIN_UP 58 0.493644 2.08704 0 4.49E−04 0.11 2533 LIN_APC_TARGETS 43 0.5227274 2.085796 0 4.63E−04 0.144 1651 REN_ALVEOLAR_RHABDOMYOSARCOMA_DN 276 0.892606

2.083815 0 4.77E−04 0.118 2738 FOURNIER_ACINAR_DEVELOPMENT_LATE_DN 19 0.6474959 2.082123 0 4.90E−04 0.121 851 PBC2_EED_UP.V1_DN 134 0.4268149 2.076228 0 5.13E−04 0.007 2312 GABP_B 143 0.4189898 2.063228 0 5.32E−04 0.013 2829 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN 125 0.4324655 2.065624 0 5.26E−04 0.151 2186 REACTOME_LICAM_INTERACTIONS 53 0.4901342 2.063811 0 5.35E−04 0.153 2277 RACTOME_IMMUNE_SYSTEM 447 0.3663814 2.06316 0 6.48E−04 0.156 2335 REACTOME_EXTENSION_OF_TELOMERES 21 0.6127662 2.061614 0 6.65E−04 0.161 2995 REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUB- 21 0.6276293 2.058993 0 7.00E−04 0.167 2626 STRATE_TO_CCT_TRIC PEART_HDAC_PROLIFERATION_CLUSTER_DN 53 0.4996137 2.05855 0 7.08E−04 0.17 2610 CHICAS_RB1_TARGETS_GROWING 158 0.4130699 2.057432 0 7.17E−04 0.173 1248 SHEPARD_CRUSH_AND_BURN_MUTANT_DN 115 0.4365805 2.055288 0 7.41E−04 0.18 1506 PIC_DCD42_REG_PATHWAY 23 0.5967745 2.051288 0 7.79E−04 0.19 2091 SAKAL_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP 56 0.4953079 2.051345 0 7.82E−04 0.19 3121 GRUETZMANN_PANCREATIC_CANCER_UP 228 0.3930303 2.046502 0 8.39E−04 0.204 2331 REACTOME_HIV_LIFE_CYCLE 24 0.4655075 2.045835 0 8.43E−04 0.204 2512 FORTSCHEGGER_PHFS_TARGETS_DN 422 0.367635 2.044175 0 8.81E−04 0.213 2579 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP 79 0.4603269 2.043856 0 8.81E−04 0.214 1582 ELK1_02 125 0.4157337 2.006724 0 9.40E−04 0.024 3202 WANG_CISPLATIN_RESPONSE_AND_XPC_UP 112 0.4272534 2.032858 0 9.47E−04 0.231 2264 KEGG_

_MEDIATED_PROTEOLYSIS 89 0.4459266 2.036673 0 9.59E−04 0.234 2913 RECTOME_CITRIC_ACID_CYCLE_TCA_CYCLE 15 0.6613815 2.035854 0 9.66E−04 0.237 1824 GENTILE_RESPONSE_CLUSTER_D3 51 0.4862784 2.03346 0 9.78E−04 0.239 3077 WSIT_ADRENOCORTICAL_TUMOR_MARKERS_UP 17 0.6444951 2.034373 0 9.95E−04 0.244 1232

indicates data missing or illegible when filed

In contrast to the results above for apoptosis and cell cycle genes, large changes were observed for differentiation and developmental gene expression in FR-treated Gαq(Q209L)-driven 92.1 cells. Most strikingly, a distinct gene cluster was downregulated dramatically (4- to ˜160-fold; FIG. 7B; circled, and Table 3). Among genes in this cluster, 38% are associated with cell differentiation and development (FIG. 7C and Table 4), as revealed by Gene Ontology analysis. More important, 42% of genes in this cluster are known targets of the polycomb repressive complex 2 (PRC2) during differentiation from embryonic stem cells (FIG. 7D and Table 5), as indicated by gene set enrichment analysis. These results were confirmed by quantitative RT-PCR analysis of FR-treated Mel202 cells (FIG. 10 ). In contrast, expression of PRC2-regulated genes in BRAF(V600E)-driven OCM-1A cells was unaffected by FR (FIG. 10 ), demonstrating specificity of FR for developmental and differentiation genes targeted by constitutively active Gαq in UM cells

The RNA-seq analyses suggested a novel mechanism for Gαq-induced oncogenesis in UM in which constitutively active Gαq antagonizes PRC2-mediated gene repression, thereby reactivating genes associated with stemness and driving de-differentiation of UM cells into a more stem-like phenotype. FR treatment inhibits constitutively active Gαq, relieves blockade of PRC2-mediated repression, re-silences these genes, and returns UM cells to a melanocytic state. Consistent with this hypothesis, we found that inhibiting the catalytic subunit of PRC2 complexes (Ezh1/2) with GSK503 maintained 92.1 cells in an undifferentiated state and blocked the ability of FR to re-differentiate these cells as indicated by morphology (FIG. 7E) and pigmentation (FIG. 7F).

A striking and unanticipated consequence of inhibiting constitutively active Gαq in UM was discovered—the repression of gene sets that control differentiation and development. Many of these repressed genes are involved in embryonic stem cell lineage specification and differentiation, and they are targets of epigenetic silencing by the polycomb repressive complex 2 (PRC2), which acts through histone H3K27 trimethylation (34-36). These repressed genes include ADRA2A (alpha-adrenergic receptor-2A) and HAND2 (heart and neural crest derivatives expressed-2). The ADRA2A gene promoter was identified in independent screens for PRC2 subunit binding and for histone H3K27 trimethylation (34-36), and ADRA2A has been linked to cancer progression and severity (37). The HAND2 gene promoter is also targeted by PRC2 binding and histone H3K27 trimethylation (34-36), especially in migrating cranial neural crest cells, where HAND2 expression distinguishes neural crest cell lineages during facial development (38). Together, these findings reveal a novel mechanism in which signaling by constitutively active Gαq in UM cells antagonizes PRC2-mediated gene silencing, thereby maintaining UM cells in a less differentiated state similar to pre-melanocytic cranial neural crest cells (38).

Materials and Methods for Examples 1-5

FR900359 was purified from A. crenata according to published methods (20). The structure of purified FR900359 relative to a commercially available equivalent (UBO-QIC; University of Bonn (Germany)) was established by NMR.

Biochemical Assays

Split luciferase assays were performed as described (24). The N-terminal portion of click beetle green luciferase (CBGN) was inserted into the αB-αC loop within the helical domain of wild type (WT) and constitutively active (Q/L) mutant forms of Gα and Gα13. Insertion of foreign proteins at this site preserves Gαfunction (40). The C-terminal region of click beetle green luciferase (CBGC) was fused to the N-termini of G131 (which was co-expressed with untagged Gγ2), RGS2, and the RGS domain of LARG, which interacts with Gal 3 only in the active GTP-bound state (41). HEK-293 cells transiently transfected with various combinations of tagged proteins were treated 18 h with vehicle(DMSO) or FR and luciferase assays were performed to measure reconstituted luciferase activity.

Assays of transcriptional reporters driven by YAP or Gα subunits were performed as described (42, 43). YAP- or Ga-driven firefly luciferase activity was normalized to Renilla luciferase expressed from a constitutive promoter.

Experiments used to measure agonist-evoked inhibition of forskolin-induced cAMP formation in Neuro2A cells were performed as described (24). Cells were transfected with a cAMP FRET reporter and pertussis toxin (PTX)-resistant forms of Gαi1, Gαi/q or Gαi/q(R54K). After cells were treated 16h with PTX to inactivate endogenously expressed Gi, FRET was used to measure inhibition of forskolin-induced cAMP formation by a CB1 cannabinoid receptor agonist (WIN 55, 212-2; WIN).

Accumulation of IP1 in UM cells was measured using the IP-One kit (CiSbio, Inc; catalog number 62IPAPEB) according to the supplier's instructions. 10,000 Mel 202 cells, 20,000 92.1 cells and 20,000 OCM 1A cells were seeded into white-bottom tissue culture grade 384-well plates. Following an overnight incubation, cells were treated with FR or DMSO and returned to the incubator. The next day, stimulation buffer was added for 1 h, after which IP1-d2 and Ab-Cryp were added, and the cells were incubated at room temperature for 60 min. Plates were read in a Synergy H4 Hybred Reader (BioTek, Winooski, Vt., USA). Standard curves were generated using reagents supplied with the kit.

Cell Culture Assays

Cells were cultured at 37.0 in 5% CO2. Human 92.1, Mel202, and OCM-1A UM cells were derived by and the generous gifts of Drs. Martine Jager (Laboratory of Ophthalmology, Leiden University), Bruce Ksander (Schepens Eye Institute, Massachusetts Eye and Ear Infirmary) and June Kan-Mitchell (Biological Sciences, University of Texas at El Paso), respectively. Cell lines were grown in RPMI 1640 medium (Life Technologies, Carlsbad, Calif.) supplemented with 10% FBS and antibiotics. Cell viability was measured using a water-soluble tetrazolium salt, WTS-8 (Bimake, Houston, Tex.), following the manufacturer's protocol. Flow cytometry for analysis of cell proliferation and apoptosis was performed at the Siteman Cancer Center Flow Cytometry Core on a FACScan analyzer (BD Biosciences, San Diego Calif., USA) using a standard propidium iodide staining protocol as described previously (44).

Immunostaining

Cell fixation was carried out by adding an equal volume of 2×fixative (PBS with 4% paraformaldehyde and 0.4% glutaraldehyde) to UM cells in RPMI growth medium. After 15 min at 37° C., cells were permeabilized with 0.1% Triton X-100 in PBS for 5 min, washed with PBS, and blocked with 2% fish gelatin (Sigma-Aldrich) in PBS. Primary and secondary antibodies were diluted in 2% fish gelatin in PBS. Primary antibodies included mouse monoclonal anti-pre-melanosomal protein (One World Lab, San Diego, Calif.), rabbit polyclonal anti-tyrosinase (One World Lab), rabbit polyclonal anti-dopachrome tautomerase (One World Lab), rabbit polyclonal anti-S100 (DakoCytomation, Denmark), and mouse monoclonal anti-BrdU (Life Technologies). Secondary antibodies were Alexa-fluor conjugates (Life Technologies), and the mounting agent was ProLong Gold (Life Technologies). Cell morphology was assessed by phase contrast imaging with an inverted microscope (Olympus IX72) using a 10×objective.

Immunoblotting

For standard immunoblots, cells were lysed and cleared in radioimmunoprecipitation assay buffer (150 mM sodium chloride, 1% Triton-X100, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate, 50 mM Tris, pH 8.0) with 1×Complete Protease Inhibitor (Roche, cat.11697498001). Histones were isolated from cells using the Active Motif Histone Purification Mini Kit (cat.40026, Active Motif, Carlsbad, Calif.). Lysates were resolved on 15% SDS-PAGE gels and transferred to Immobilon(P) PVDF membrane (Milipore, cat.IPVH00010). Membranes were blocked with 5% w/v milk in TBST (25 mM Tris pH 7.2, NaCl 150 mM, 2.7 mM KCl, 0.1% v/v Tween 20) and incubated with primary antibodies. Membranes were washed with TBST at least three times and incubated with IRDye 680 Goat anti-rabbit and IRDye 800 Goat anti-mouse (LI-COR, Lincoln, Nebr.). Following incubation, membranes were washed at least three times with TBST and signals were detected using LI-COR Odyssey model 9120 imaging system (LI-COR). Primary antibodies used for immunoblots were: anti-EE (Covance, cat. MMS-115P, lot E12BF00285), anti-Actin C4 (Millipore, cat. MAB1501), anti-Histone H3 (clone A3S, cat.05-928, Millipore) and Anti-histone H3-trimethyl-K27 (cat.6002, Abcam).

Gene Expression Analysis

92.1 UM cells were treated with 100 nM FR or vehicle (DMSO) in RPMI growth medium and collected after 1 and 3 d of treatment. RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol and including the optional DNase I treatment step. RNA quality was assessed on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, Calif., USA). mRNA was extracted from total RNA using a Dynal mRNA Direct kit, fragmented and reverse transcribed to double stranded cDNA with random primers before addition of adapters for library preparation. Library preparation and HiSeq2500 sequencing were performed by the Washington University Genome Technology Access Center (gtac.wustl.edu). FastQ files were aligned to the transcriptome and the whole-genome with STAR. Biologic replicates were simultaneously analyzed by edgeR and Sailfish analyses of gene-level/exon-level features. Unexpressed genes and exons were removed from the analyses. Unsupervised principal component analysis and volcano plots were generated in Bioconductor using edgeR. Significance Analysis of Microarrays (SAM), Version 4.0 was used to generate a ranked gene list, and a threshold of q<10% and fold-change >2.0 was then used to select the most highly significant genes that were down regulated in FR-treated versus vehicle control cells. This list was used as signature gene sets for Gene Ontology (GO) analysis and Gene Set Enrichment Analysis (GSEA) (45). GO groups were assembled by merging the lists of genes from related GO terms that were significantly enriched in the signature gene set. Significant gene sets from GSEA analyses were combined such that genes associated with multiple related signatures were only counted once and each gene was assigned only to a single combined groupbased on the signature with the highest enrichment score for that gene. Significant gene expression changes were validated in all three UM cell lines by qPCR using fast SYBR Green Mastermix (Fisher Scientific) following the manufacturers' protocol. GAPDH was used as an endogenous control. Primer sets used for the assay are listed in table 6.

TABLE 2 Gene Set Enrichment Negative Correlation NOM FDR FWER RANK NAME SIZE ES NES p-val q-val p-val AT MAX KEGG_RIBOSOME 77 −0.8474475 −4.11456 0 0 0 1165 REACTOME_PEPTIDE_CHAIN_ELONGATION 78 −0.8362932 −4.040971 0 0 0 1165 REACTOME_3_UTR_MEDIATED_TRANSLA- 93 −0.7894343 −4.002007 0 0 0 806 TIONAL_REGULATION REACTOME_INFLUENZA_VIRAL_RNA_TRAN- 89 −0.7620774 −3.777758 0 0 0 1414 SCRIPTION_AND_REPLICATION REACTOME_NONSENSE_MEDIATED_DECAY_EN- 90 −0.7575414 −3.775522 0 0 0 806 HANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_SRP_DEPENDENT_COTRANS- 88 −0.7586833 −3.77252 0 0 0 1165 LATIONAL_PROTEIN_TARGETING_TO_MEMBRANE

_SERUM_AND_RAPAMYCIN_SEN- 5

−0.8275592 −3.744492 0 0 0 890 SITIVE_GENES REACTOME_TRANSLATION 117 −0.69

806 −3.614177 0 0 0 1222 REACTOME_FORMATION_OF_THE_TERNA- 42 −0.7636944 −3.333641 0 0 0 1414 RY_ COMPLEX_AND_SUBSEQUENT- LY_THIS_43S_COMPLEX

ATI_G2M_ARREST_BY_2METHOXYESTERADIOL_DN 69 −0.6813395 −3.252417 0 0 0 1562 CHNG_MULTIPLE_MYELOMA_HYPERLOID_UP 40 −0.7651164 −3.199398 0 0 0 1320 KRIGE_AMINO_ACID_DEPRIVATION 24 −0.8503655 −3.140422 0 0 0 1094 REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BIND- 48 −0.725141 −3.124917 0 0 0 1414 ING_OF_THE_CAP_BINDING_COM- PLEX_AND_

_AND_SUBSEQUENT_BIND- ING_TO_45S ALK_DN.V1_UP 56 −0.6754234 −3.122742 0 0 0 985

ANGES_SERUM_RESPONSE_TRANSLATION 26 −0.7377167 −3.031653 0 0 0 875 REACTOME_INFLUENZA_LIFE_CYCLE 117 −0.5825156 −3.005197 0 0 0 806 REACTOME_METABOLISM_OF_MRNA 150 −0.5385245 −2.898579 0 0 0 806

_MAMMARY_STEM_CELL_UP 89 −0.5578858 −2.803973 0 0 0 1222 ZHANG_TLX_TARGETS_UP 64 −0.5840745 −2.79729

0 0 0 1627 FLOTHO_PEDIATRIC_A

_THERA- 39 −0.6667184 −2.788914 0 0 0 1090 PY_RESPONSE_UP

_INTESTINE_PROBIOTICS_24HR_DN 160 −0.483478 −2.683889 0 0 0 1198 ABE_INNER_

27 −0.7179842 −2.671323 0 0 0 1098 MCMURRY_TP53_MRAS_COOPERATION_RESPONSE_DN 31 −0.5834503 −2.650262 0 0 0 1285 PENG_LEUCINE_DEPRIVATION_UP 100 −0.5277748 −2.6299

9 0 0 0 1633 HU_GENOTOXIC_DAMAGE_24HR 24 −0.7261035 −2.629237 0 0 0 834 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP 44 −0.5992472 −2.602829 0 0 0 1256 REACTOME_METABOLISM_OF_RNA 180 −0.4550802 −2.581436 0 0 0 806 PACHER_TARGETS_OF_IGF1_AND_IGF2_UP 27 −0.679906 −2.571271 0 0 0 881

_RESPONSE_TO_

_UP 35 −0.6332173 −2.557885 0 0 0 837 PODAR_RESPONSE_TO_ADAPHOSTIN_UP 104 −0.5083627 −2.557086 0 0 0 1633 TARTE_PLASMA_CELL_VS_PLASMABLAST_UP 184 −0.4464259 −2.5482 0 0 0 1390

SON_SICKLE_CELL_DISEASE_DN 116 −0.4751957 −2.531408 0 0 0 875 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP 106 −0.4918961 −2.5305 0 0 0 1582

EN_INTESTINE_PROBIOTICS_6HR_UP 47 −0.5729876 −2.518115 0 0 0 733

_TNC_TARGETS_UP 10

−0.4853156 −2.514798 0 0 0 2047 LEE_NEURAL_CREST_STEM_CELL_DN 60 −0.5112373 −2.510382 0 0 0 1537 BRACHAT_RESPONSE_TO_CAMPIOTHEON_UP 16 −0.7423251 −2.491617 0 0 0 1429 MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 139 −0.4619398 −2.475651 0 0 0 1429 MOLLEMAN_ASPARAGINAS_RESISTANCE_

_ALL_UP 19 −0.7230168 −2.468087 0 0 0 1222 KRAS.LUNG.BREAST_UP.V1_DN 40 −0.5628054 −2.3475 0 0 0 1983 Il1S_UP.V1_DN 63 −0.5127742 −2.342012 0 0 0 1872 YAO_TEMPORAL_RESPONSE_TO_PROGESTER- 47 −0.5619978 −2.458571 0 4.80E−05 0.002 1426 ONE_CLUSTER_O CHIBA_RESPONSE_TO_TSA_UP 28 −0.6260312 −2.4359 0 6.93E−05 0.003 471

_RESPONSE_TO_

_UP 158 −0.4429056 −2.428607 0 9.01E−05 0.004 1719 POMERPY_MEDULOBLASTOMA_DESMO- 31 −0.6005085 −2.387366 0 9.65E−05 0.005 911 PLASIC_VS_CLASSIC_DN REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION 19 −0.6974551 −2.393741 0 9.85E−05 0.005 721 HSIAO_HOUSEKEEPING_GENES 279 −0.398129 −2.395038 0 1.01E−04 0.005 1367 ONDONNELL_TARGETS_OF_MYC_AND_TFRC_UP 47 −0.5322069 −2.403383 0 1.03E−04 0.004 1390 AFTER_

_TARGETS_UP 93 −0.4737549 −2.403383 0 1.05E−04 0.005 1518 MIKKELSEN_NPC_HCP_WITH_

27ML3 103 −0.4727085 −2.507248 0 1.08E−04 0.005 1886 WINZLN_DEGRADED_VIA_

43 −0.5497911 −2.408297 0 1.10E−04 0.005 1303 BENPORATH_ES_WITH_H3K27ME3 410 −0.381772 −2.371255 0 1.27E−04 0.007 1922 HELLER_SILENCED_BY_METHYLATION_DN 69 −0.4980554 −2.3798 0 1.30E−04 0.007 1298 KATSANOU_FLAVL1_TARGETS_UP 79 −0.4901621 −2.383254 0 1.32E−04 0.007 817 KOBAYASHI_EGFR_SIGNALING_24HR_UP 58 −0.5187423 −2.367372 0 1.43E−04 0.008 1592

_TP53_TARGETS 21 −0.5636328 −2.34865 0 1.56E−04 0.009 1584 MARTENS_TRETINOIN_RESPONSE_UP 237 −0.4094868 −2.352606 0 1.59E−04 0.009 1471 NUTT_

M_VS_AO_GUMA_DN 31 −0.5890119 −2.34034 0 2.20E−04 0.013 1225 KASLER_HDAC7_TARGETS_2_DN 21 −0.6502378 −2.320462 0 2.23E−04 0.016 802 WEST_ADRENOCORTICAL_TUMOR_DN 261 −0.3968828 −2.322684 0 2.78E−04 0.016 1262 NEPORATH_PRC2_TARGETS 232 −0.4077365 −2.323629 0 2.83E−04 0.016 1922 MIKKELSEN_ES_ICP_WITH_

_AND_

−0.5719411 −2.286906 0 4.09E−04 0.025 1655 OSMAN_BLADDER_CANCER_DN 220 −0.3983562 −2.286096 0 4.18E−04 0.026 1356 LEE_BMP2_TARGETS_UP 367 −0.3741874 −2.283134 0 4.26E−04 0.027 1707

_BRAIN_HCP_WITH_

91 −0.4481216 −2.25685 0 5.22E−04 0.035 1852 CORRE_MULTIPLE_MYELOMA_UP 29 −0.5666021 −2.253276 0 5.28E−04 0.036 717 DELVS_THYROID_CANCER_DN 118 −0.4291295 −2.252387 0 5.30E−04 0.035 1760 MIKKELSEN_M

_HCP_WITH_N3K27ME3 146 −0.4149404 −2.264092 0 5.39E−04 0.035 1688 MEL1B_DN.V1_DN 68 −0.4482245 −2.12524 0 6.14E−04 0.002 1515 OSADA_ASC11_TARGETS_UP 21 −0.6239096 −2.23151 0 6.92E−04 0.048 1445 BRACHAT_RESPONSE_TO_METHOTREXATE_UP 17 −0.6758122 −2.233308 0 7.02E−04 0.048 1314 ATM_DN.V1_UP 55 −0.4773785 −2.129868 0 7.37E−04 0.002 1859 VARELA_ZMPSTE24_TARGETS_UP 21 −0.6318697 −2.222122 0 7.49E−04 0.053 1748

_NPC_HCP_WITH_

_AND_

129 −0.4086753 −2.220779 0 7.65E−04 0.055 1700 KRAS.800.LUNG.BREAST_UP.V1_DN 85 −0.4222526 −2.084648 0 7.86E−04 0.004 1867 CHANG_CORE_SERUM_RESPONSE_DN 125 −0.4167168 −2.209614 0 8.19E−04 0.059 1534 ZHAN_MULTIPLE_MYELOMA_CD1_UP 26 −0.5883277 −2.202799 0 8.22E−04 0.061 1094 GENTILE_UV_LOW_DOSE_UP 17 −0.6674633 −2.200004 0 8.23E−04 0.062 1462 HELLE

_SILENCED_DURING_TUMOR_ANGIOGENESIS 32 −0.5556766 −2.204214 0 8.34E−04 0.061 1098 RICKMAN_HEAD_AND_NECK_CANCER_

15 −0.6841369 −2.204823 0 8.46E−04 0.061 2000

ELA_DN.V1_UP 54 −0.4576916 −2.084719 0 8.84E−04 0.004 1678

UP.V1_DN 75 −0.4348109 −2.336282 0 9.21E−04 0.002 1508 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN 35 −0.5231197 −2.180453 0 9.84E−04 0.078 1867 REACTOME_AMINO_ACID_TRANS- 20 −0.6054498 −2.182732 0 9.85E−04 0.081 992 PORT_ACROSS_THE_PLASMA_MEMBRANE ZHAN_MULTIPLE_MYELOMA_HP_UP 28 −0.5562334 −2.17634 0 9.93E−04 0.081 1465 KINSEY_TARGETS_OF_

_

_FUSION_DN 192 −0.3867057 −2.179024 0 9.94E−04 0.08 1687

_

_TARGETS 393 −0.3540429 −2.181025 0 9.97E−04 0.078 1922 MTOR_UP.N4.Vl_DN 89 −0.4243262 −2.0919 0 0.0010103 0.004 2035 GARGALOVIC_RESPONSE_TO_OXI- 16 −0.6794893 −2.15588

0 0.00114316 0.095 1394 DIZED_PHOSPHOLIPIDS_RED_UP

_RESPONSE_TO_CISPLATIN 15 −0.

807054 −2.160356 0 0.0012011 0.107 1314 BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN 26 −0.5759184 −2.162662 0 0.00120454 0.101 1534 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP 246 −0.370676 −2.163329 0 0.00120818 0.101 1120 ZHANG_TLX_TARGETS_60HR_UP 170 −0.388943 −2.15

292 0 0.00126072 0.109 1464 CHO_NRAA1_TARGETS 18 −0.6221408 −2.153668 0 0.00127573 0.109 985 MODY_HIPPOCAMPUS_PRENATAL 30 −0.5418804 −2.139189 0 0.00153791 0.135 7

_VAV3_PROSTATE_CARCINOGENESIS_UP 37 −0.5153462 −2.124477 0 0.001782

0.159 442 SNFS_DN.V1_DN 64 −0.4239907 −1.965274 0 0.00186859 0.011 1747

_METHYLATED_DE_NOVO_IN_CANCER 34 −0.5272919 −2.11

667 0 0.00

05058 0.184 2277

_METASTASIS_DN 88 −0.4197548 −2.108774 0 0.00210896 0.19 2181 MAN_INK_SIGNALING_DN 20 −0.5953203 −2.10681 0 0.00218612 0.199

ACEVEDO_

_TARGETS_IN_PROS- 142 −0.

862232 −2.104925 0 0.00228857 0.204 1676 TATE_CANCER_MODEL_DN ODONNELL_TFRC_TARGETS_UP 196 −0.3710412 −2.095922 0 0.00239025 0.223 1526

_

_TARGETS_DN 31 −0.5304294 −2.089082 0 0.00252141 0.237 1008

_DN_MEL18_

_UP 68 −0.4154021 −1.94875 0 0.00259214 0.017 708 NABA_SECRETED_FACTERS 75 −0.4331841 −2.080575 0 0.00276229 0.26 2139

_DN.V1_UP 36 −0.4718207 −1.93928

0 0.00278338 0.02 2016

_DN_

_DN.V1_DN 74 −0.405831 −1.91433

0 0.00284814 0.024 1582

_RESPONSE_TO_IR_2HG_UP 31 −0.5168331 −2.07614 0 0.00289417 0.272 844 KRAS.KIDNEY_

_UP 67 −0.4055116 −1.

231094 0 0.002

5347 0.023 1926 KRAS.BREAST_

_DN 47 −0.436286 −1.902803 0 0.00299866 0.027 1983

BAUER_MYOGENIC_TAR- 23 −0.5719996 −2.06800

0 0.0031819 0.298 181 GETS_OF_PAX3_FOXO1_FUSION REACTOME_METABOLISM_OF_PROTEINS 281 −0.3509132 −2.05310

0 0.00360166 0.333 902

_RESPONSE_TO_CISPLATIN_UP 25 −0.5415465 −2.049847 0 0.00367513 0.341 1012

_

_DN 80 −0.

910255 −1.879492 0 0.00375577 0.039 1582

_

_TARGETS 407 −0.3305 −2.0

566 0 0.00378124 0.352 1922 VECCHI_GASTRIC_CANCER_EARLY_DN 138 −0.37

3293 −2.04198

0 0.00388

8 0.363 1683 COLIN_PILOCYTIC_ASTROCYTO- 23 −0.5577416 −2.040834 0 0.00389292 0.368 1004 MA_VS_GLIOBLASTOME_UP KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 47 −0.4683

86 −2.036092 0 0.00409951 0.385 1745 NABA_MATRISOME 332 −0.3330154 −2.033819 0 0.00411733 0.392 1622

_NF1_TARGETS_DN

−0.4710282 −2.033925 0 0.00413844 0.392 1683 WARTERS_IR_RESPONSE_SGY 24 −0.548868

−2.031

34 0 0.00418851 0.4 1278 CHANDRAN_METASTASIS_TOP50_DN 33 −0.5006422 −2.028088 0 0.00435094 0.417 1145 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSI- 85 −0.412

618 −2.18757 0 0.00476

27 0.45 1663 TION_DN NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CEN- 359 −0.33

6271 −2.005686 0 0.00534163 0.487 1642 TRAL_DN TSENG_ADIPOGENIC_POTENTIAL_DN 22 −0.4376177 −1.996347 0 0.0058487

0.52 1162 DIA2_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN

9 −0.4327

23 −1.989476 0 0.00615224 0.547 1738

_TLX1_TARGETS_DN 79 −0.4039654 −1.985129 0 0.00630517 0.564 1335 SENESE_MDAC1_TARGETS_DN 130 −0.3720098 −1.985254 0 0.00635953 0.564 1581 MCBRYAN_PUBERTAL_BREAST_4_

_UP 128 −0.3700548 −1.985129 0 0.0063

14 0.571

_AMPLIFIED_IN_LUNG_CANCER 107 −0.3859681 −1.985254 0 0.00658682 0.583 1342 KEGG_GLYCINE_SERINE_AND_THREO- 16 −0.5888243 −1.983151 0 0.00725142 0.612 1228 NINE_METABOLISM VEG

_A_UP.V1_UP 86 −0.

7239 −1.978049 0 0.0072629 0.079 1874

ATO_SILENCED_BY_METHYLA- 22 −0.

36463 −1.967282 0 0.00804425 0.654 729 TION_IN_PANCREATIC_CANCER_2 WANG_HCP_PROSTATE_CANCER 67 −0.4152

23 −1.81014

0 0.00817478 0.662 1557 YANASHIYA_LIVER_CANCER_WITH_EPCAM_UP 43 −0.4

2825 −1.9

973 0 0.00833

24 0.671 806 ONKEN_LIVEAL_MELANOMA_DN 357 −0.3213334 −1.952216 0 0.00

00

99 0.698 1090 BLI1_ND, V1_DN 80 −0.3678445 −1.94856 0 0.00905821 0.101 1215 HILLION_HMGA1_TARGETS 42 −0.4412338 −1.980038 0 0.00919841 0.712 834

_(——)GR_TARGETS_DN 57 −0.42499

4 −1.788332 0 0.00959250 0.731 1537

_TARGETS_OF_NUP98_HOXA- 67 −0.4071266 −1.

34745 0 0.00

618 0.729 1616 METHYLATION_FUSION_

_UP SATO_SILENCED_BY_METHYLA- 178 −0.34

9559 −1.927633 0 0.0098

593 0.741 870 TION_IN_PANCREATIC_CANCER_1 WANG_RESPONSE_TO_

_INHIBITOR_

_UP 173 −0.3449602 −1.92858 0 0.00986767 0.743 1476

_RESPONSE_TO_

_24HR_UP 417 −0.311824

−1.923871 0 0.01033876 0.762 1656

_INTESTINE_PROBIOTICS_2HR_UP 20 −0.5457836 −1.923048 0 0.01058532 0.776 623 NABA_

_MATRISOME 106 −0.3700458 −1.91720

0 0.01068174 0.783 1995

_DN.V1_UP 60 −0.3745471 −1.913324 0 0.0108184 0.13 1456 MIKKELSEN_NPC_HCP_WITH_

_

113 −0.3639965 −1.911882 0 0.01098524 0.791 1236 ZWANG_EGF_INTERVAL_DN 105 −0.3712006 −1.754636 0 0.110

864 0.797 1574 RAF_Up, V1_DN 115 −0.336931

−1.90749

0 0.01116835 0.129 1252 ESC_V6.5_UP_

_UP 99 −0.3398488 1.

04332 0 0.01148195 0.158 2255 EPS14_DN.V1_UP 68 −0.

689693 1.732568 0 0.01187341 0.154 1855 KRAS.600_UP.V1_UP 98 −0.3459822 −1.742945 0 0.01187341 0.147 1926 ZHANG_TIX_TARGETS_36HR_UP

−0.3453688 −1.888205 0 0.01262035 0.8

1627 SMID_BREAST_CANCER_BASAL_DN 329 −0.3126253 −1.883826 0 0.01296399 0.87 1675

QUEST_STEM_CELL_UP 120 −0.3570578 −1.87823

0 0.1352501 0.879 1098 CHARAFE_BREAST_CANCER_LU- 207 −0.3233547 −1.878

3 0 0.013

1267 0.879 2112 MINAL_VS_MESENCHYMAL_UP

ZONYI_RESPONSE_TO_LEUKOTRI- 20 −0.5306243 −1.874163 0 0.01387

1 0.895 1342 ENE_AND_THROMBIN SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN 19 −0.5454792 −1.872329 0 0.01400287 0.898 829 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN 292 −0.3103153 −1.883277 0 0.01506865 0.915 1225

_

_TARGETS_SILENCED_BY_METHYLATION_DN 156 −0.341619 −1.860008 0 0.01519207 0.923 1722

_TP53_TARGETS_UP 30 −0.4737572 −1.858808 0 0.01528555 0.925 1234

_LVAD_SUPPORT_OF_FAILING_HEART_UP 61 −0.3964793 −1.860017 0 0.01529202 0.923 1953 SENESE_HDAC2_TARGETS_DN 58 −0.4105108 −1.857179 0 0.01540092 0.927 1265

_THYROID_CANCER_CLUSTER_3 18 −0.5378169 −1.847228 0 0.01637045 0.94

1571 ONDER_CDH1_TARGETS_2_DN 205 −0.3275371 −1.842224 0 0.01651001 0.949 1698 NABA_MATRISONE_ASSOCIATED 226 −0.3210322 −1.839573 0 0.01657065 0.953 1622 GROSS_HYPOXIA_VIA_ELK3_DN 91 −0.3727931 −1.83489

0 0.01703481 0.958 1196

_BREAST_CARCINOMA_METAPLA- 39 −0.4381889 −1.820886 0 0.01885336 0.973 1554 STIC_VS_DUCTAL_DN KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 31 −0.4029248 −1.816281 0 0.01934519 0.575

BOYLAN_MULTIPLE_MYELOMA_PCA1_UP 36 −0.4387771 −1.811622 0 0.02000

1 0.98 1120 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP 84 −0.370705 −1.809931 0 0.02004517 0.981 1820 KAN_RESPONSE_TO_ARSENIC_

77 −0.3679383 −1.7

403 0 0.0223979

0.992 1177 TANG_SENESCENCE_TP53_TARGETS_UP 19 −0.5184155 −1.789191 0 0.02250124 0.992 584

_01 68 −0.43

0142 −2.071792 0 0.02263345 0.022 1780 PHONG_TNF_TARGETS_UP

9 −0.4511476 −1.784894 0 0.02298985 0.994 1760 CHEN_HOXA5_TARGETS_9HR_UP 119 −0.3414734 −1.77

823 0 0.02391435 0.994 1862 WANG_SMARCI1_TARGETS_UP 145 −0.3286828 −1.7

7

4 0 0.02524347 0.996 1433 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP 158 −0.3244276 −1.757059 0 0.0267891 0.997 1458

_MMP14_TARGETS_UP 134 −0.328

391 −1.757222 0 0.02688

0.997 1621 OCT1_01 106 −0.363

927 −1.849983 0 0.02692084 0.166 1738 HAMAI_APOPTOSIS_VIA_TRAIL_DN 99 −0.3456973 −1.757245 0 0.027007

4 0.997 1511 CAIRO_HEPATOBLASTOMA_CLASSES_DN 103 −0.3429401 −1.751814 0 0.02741138 0.998 1338 ZHU_CMV_ALL_DN 78 −0.

619418 −1.743817 0 0.02855004 0.998 1119 CHOP_01 128 −0.3492407 −1.858297 0 0.0286299 0.153 1747 PTEN_DN.V2_UP 57 −0.3445246 −1.

94083 0 0.02868814 0.435 1687

_01 105 −0.3707155 −1.876172 0 0.02933803 0.133 1777

25_02 114 −0.33732 −1.773233 0 0.02952358 0.291 1489 AREB6_02 113 −0.3688074 −1.902379 0 0.02982211 0.107 1415 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN 58 −0.3815674 −1.732381 0 0.03007418 0.998 1210 DURAND_STROMA_S_UP 152 −0.3195942 −1.733426 0 0.03008104 0.998 2007 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN 195 −0.3010991 −1.732732 0 0.0301192 0.998 1537 KARLSSON_TGFB1_TARGETS_DN 130 −0.3276407 −1.72

512 0 0.03020474 0.998 1387

01 45 −0.4136769 −1.777444 0 0.03104507 0.282 1822 OCT

_Q6 112 −0.34622

−1.799742 0 0.03116295 0.238 1496 MEF2_03 108 −0.

427669 −1.779354 0 0.03

73754 0.279 1097

_BREAST_DUCTAL_CARCINO- 78 −0.3446056 −1.70

7

0 0.03375342 0.999 2141 MA_VS_DUCTAL_NORMAL_DN NABA_

_GLYCOPROTEINS 78 −0.3494785 −1.710854 0 0.03391476 0.999 1267

_UNKNOWN 182 −0.3083577 −1.726828 0 0.034

4571 0.399 1452 TATA_01 95 −0.3530411 −1.746497 0 0.03502827 0.35 1640 ONDER_CDH1_TARGETS_1_UP 85 −0.3428228 −1.70

843 0 0.03536654 0.999 1592 RODWELL_AGING_KIDNEY_NO_BLOOD_UP 106 −0.3340731 −1.70463 0 0.03554897 0.999 902 MEISSNER_NPS_HCP_WITH_

218 −0.2970

3

−1.694809 0 0.03696674 0.999 1487

_EWING_SARCOMA_PROGENITOR_UP 204 −0.2994

11 −1.694891 0 0.03710773 0.999 1688 REACTOME_GPCR_LIGAND_BINDING 77 −0.3492122 −1.691504 0 0.03761812 0.999 1510 AFT

_Q6 135 −0.3167327 −1.708413 0 0.03762414 0.47 1390 MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED 178 −0.344891 −1.688832 0 0.0378

327 0.999 891 GAUSSMANN_

_AF4_FUSION_TARGETS_

_UP 107 −0.37

00

−1.681214 0 0.03865468 0.999 1171 MEISSNER_BRAIN_HCP_WITH_

_AND_

494 −0.2660

4 −1.682982 0 0.03865

0.999 1587 WONG_ADULT_TISSUE_STEM_MODULE 373 −0.24242

−1.

34

0 0.03870441 0.999 17

CRABP

_01 94 −0.3372097 −1.692837 0 0.03904044 0.522 1807 MEF2_02 97 −0.3755514 −1.9043

4 0 0.0

908205 0.106 1817 WANG_

_TARGETS 122 −0.3172455 −1.676372 0 0.03996525 0.999 1585 SOX

_01 140 −0.31

98 −1.693732 0 0.040

2704 0.521 1321

_YBX1_TARGETS_DN 212 −0.2925394 −1.

8706 0 0.04115818 0.999 1298 MIKKELSEN_NPC_ICP_WIHT_

208 −0.2916188 −1.666103 0 0.04180007 1 1286

_01 123 −0.3105689 −1.646637 0 0.

189491 0.674 1271 SRY_02 119 −0.31634

−1.649142 0 0.04275158 0.672 1313

_UNKNOWN 333 −0.2775641 −1.676503 0 0.0436862

0.579 1777 FO

O3_01 113 −0.

20

756 −1.670072 0 0.04394717 0.603 1899 OCT1_05 105 −0.3237793 −1.65407

0 0.0440

56 0.6

1271

_EXTRADIOL_RESPONSE_24HR_DN 309 −0.2760787 −1.650879 0 0.04567584 1 1663 GATA1_04 100 −0.3178839 −0.

226 0 0.04720975 0.755 1581

_01 127 −0.2

7850

−0.158209 0 0.04985837 0.901 1271

_TAMOXIFEN_RESISTANCE_DN 137 −0.3024071 −1.635857 0 0.0501198 1 1304

_01 105 −0.3122923 −1.604354 0 0.050928

4 0.806 1834

_UNKNOWN 440 −0.25181

−1.

26 0 0.05103919 0.898 1899 ECEVEDO_LIVER_CANCER_WITH_

_UP 94 −0.32

92 −1.63057 0 0.05167929 1 1220 FAXA_02 111 −0.

123 −1.

710

0 0.05282452 0.895 1439 CEBP_C 103 −0.3089

72 −1.

713

0 0.0539347 0.893 1132 MANALO_HYPOXIA_UP 125 −0.3081693 −1.

22452 0 0.05394896 1 1438

_Q6 101 −0.3074716 −0.31.570722 0 0.05465443 0.865 1889

_01 105 −0.30

−1.543776 0 0.055303

0.845 1777 DAZARD_RESPONSE_TO_UV_NHEK_UP 133 −0.2978842 −1.

03364 0 0.05

26026 1 1867 FOXJ2_02 106 −0.2907478 −1.5132364 0 0.06134814 0.943 1314

_

_

361 −0.242

834 −1.4914

8 0 0.00

867 0.984 1267

_

_ONCOGENIC_SIGNATURE 149 −0.7680557 −1.571815 0 0.06886319 1 1342 CHICAS_

_TARGETS_CONFLUENT 324 −0.2638294 −1.571262 0 0.06886729 1 881

_Q6 108 −0.

5

8 −1.47767 0 0.02037452 0.993 1486 AMUNDSON_RESPONSE_TO_ARSENITE 141 −0.2875814 −1.549565 0 0.07575028 1 1633

_UV_RESPONSE_KERATINOCYTE_UP 283 −0.2620121 −1.551263 0 0.07628742 1 1498

_RESPONSE_TO_

_UP 236 −0.2645626 −1.543008 0 0.0774

664 1 1621 MIKKELSEN_ES_

_WITH_

288 −0.25425

4 −1.533512 0 0.0806

149 1 1567

_

_TARGETS_DN 370 −0.243

075 −1.520984 0 0.08460882 1 1829

_UNKNOWN 490 −0.2266161 −1.410288 0 0.0

057047 0.999 1843

_UNKNOWN 168 −0.

027 −1.

674 0 0.0922318

0.999 1777

_HEART_ATRIUM_VS_VENTRICLE_UP 144 −0.2784034 −1.497008 0 0.0

37

81 1 1710

_AGING_BRAIN_UP 172 −0.2649863 −1.49

99 0 0.0

549277 1 1576

_

_TAGETS 129 −0.2

41817 −1.48209

0 0.09775172 1 2060

_PROSTATE_CANCER_DN 242 −0.2

23566 −1.47928

0 0.09844034 1 1602

_

_TARGETS_UP 155 −0.2

−1.47677

0 0.09887995 1 1297 MARTENS_TRETINOIN_RESPONSE_DN 401 −0.236

414 −1.45397 0 0.10912863 1 962

_ENDOCRINE_THERAPY_RESISTANCE_1 297 −0.2420859 −1.447294 0 0.1191201 1 1256 RODRIGUES_THYROID_CARCINOMA_POOR- 454 −0.2258331 −1.399758 0 0.13657138 1 1642 LY_DIFFERENTIATED_DN KIM_BIPOLAR_DISORDER_OLIGODENDRO- 411 −0.221016 −1.39767 0 0.13771

79 1 1167 CYTE_DENSITY_CORR_UP

indicates data missing or illegible when filed

TABLE 3 FR Responsive Downregulated Genes Adjusted Fold

_ID Gene name Description P-value Change

indicates data missing or illegible when filed

TABLE 4 FR responsive Downregulated Genes GO # Genes in # Genes in FDR Gene Set Name Gene Set (K) overlap (k) k/K p-value q-value GO_NEUROGENESIS 1402 92 0.0656 1.13E−33 6.97E−30 GO_CELL_DEVELOPMENT 1426 91 0.0638 2.19E−32 6.76E−29 GO_NEURON_DIFFERENTIATION 874 70 0.0801 7.09E−31 1.46E−27 GO_REGULATION_OF_MULTICELLULAR_ORGANISMAL_DEVELOPMENT 1672 95 0.0568 6.71E−30 1.04E−26 GO_TISSUE_DEVELOPMENT 1518 90 0.0593 1.15E−29 1.42E−26 GO_EMBRYO_DEVELOPMENT 894 69 0.0772 1.79E−29 1.84E−26 GO_REGULATION_OF_CELL_DIFFERENTIATION 1492 83 0.0

6 1.58E−25 1.33E−22 GO_ORGAN_MORPHOGENESIS 841 62 0.0737 1.73E−25 1.33E−22 GO_EMBRYONIC_MORPHOGENESIS

50 0.0928 3.90E−25 2.67E−22 CO_REGULATION_OF_CELL_PROLIFERATION 14

82 0.0548 8.29E−25 5.11E−22 GO_TUBE_DEVELOPMENT 552 50 0.0006 1.14E−24 6.40E−22 GO_EPITHELIUM_DEVELOPMENT 94

64 0.0677 2.76E−24 1.42E−21 GO_POSITIVE_REGULATION_OF_CELL_COMMUNICATION 1532 80 0.0522 6.78E−23 3.21E−20 GO_TISSUE_MORPHOGENESIS 533 47 0.0882 9.19E−23 4.05E−20 GO_UROGENITAL_SYSTEM_DEVELOPMENT

36 0.1204 3.28E−22 1.28E−19 GO_INTRACELLULAR_SIGNAL_TRANSDUCTION 1572 80 0.0509 3.33E−22 1.28E−19 GO_NUCLEIC_ACID_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY 1199 29 0.0575 4.00E−22 1.45E−19 GO_ANATOMICAL_STRUCTURE_FORMATION_IN- 957 61 0.0637 7.51E−22 2.57E−19 VOLVED_IN_MORPHOGENESIS GO_CENTRAL_NERVOUS_SYSTEM_DEVELOPMENT 872 58 0.0665 1.04E−23 3.37E−19 GO_MORPHOGENESIS_OF_AN_EPITHELIUM 400 40 0.1000 1.59E−21 4.89E−19 GO_CELL_MORPHOGENESIS_INVOLVED_IN_DIFFERENTIATION 513 44 0.0858 6.52E−21 1.92E−18 GO_POSITIVE_REGULATION_OF_MULTICELLULAR_OR- 1395 72 0.0516 2.20E−20 6.17E−18 GANISMAL_PROCESS GO_POSITIVE_REGULATION_OF_BIOSYNTHETIC_PROCESS 1805 83 0.0

60 2.59E−20 7.65E−18 GO_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION 1656 79 0.0477 2.98E−20 7.65E−18 GO_POSITIVE_REGULATION_OF_GENE_DEXPRESSION 1733 81 0.0467 3.25E−20 8.01E−18 GO_CARDIOVASCULAR_SYSTEM_DEVELOPMENT 788 53 0.0

73 3.87E−20 8.84E−18 GO_CIRCULATORY_SYSTEM_DEVELOPMENT 788 53 0.0

73 3.87E−20 8.84E−18 GO_MOVEMENT_OF_CELL_OR_SUBCELLULAR_COMPONENT 1275 68 0.0533 4.55E−20 1.05E−17 GO_RESPONSE_TO_EXTERNAL_STIMULUS 1821 83 0.0456 4.95E−20 1.05E−17 GO_NEURON_PROJECTION_DEVELOPMENT 545 44 0.0807 6.81E−20 1.40E−17 GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMBRANE 1649 78 0.0473 8.67E−20 1.68E−17 GO_REGULATION_OF_ANATOMICAL_STRUCTURE_MORPHOGENESIS 1021 60 0.0588 8.73E−20 1.68E−17 GO_NEURON_DEVELOPMENT 687 49 0.0713 9.44E−20 1.76E−17 DO_REGULATION_OF_TRANSPORT 1804 82 0.0455 1.00E−19 1.82E−17 GO_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT 750 51 0.0680 1.27E−19 2.24E−17 GO_POSITIVE_REGULATION_OF_RESPONSE_TO_STIMULUS 1929 85 0.0441 1.36E−19 2.33E−17 GO_CELL_PROJECTION 1786 81 0.0454 1.96E−19 3.27E−17 GO_TUBE_MORPHOGENESIS 323 34 0.1053 3.48E−19 5.64E−17 GO_CELL_PROJECTION_ORGANIZATION 902 55 0.0610 6.25E−19 9.89E−17 GO_EMBRYONIC_ORGAN_DEVELOPMENT 405 37 0.0911 1.19E−18 1.83E−16 GO_RECEPTION_BINDING 1476 71 0.0481 1.84E−18 2.77E−16 GO_NEURON_PART 1268

0.0514 2.21E−18 3.24E−16 GO_CELLULAR_COMPONENT_MORPHOGENESIS 900 54 0.0600 2.68E−18 3.84E−16 GO_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION 1791 79 0.0441 2.

3E−18 3.97E−16 GO_APPENDAGE_DEVELOPMENT 169 25 0.1479 5.36E−18 7.19E−16 GO_LIMB_DEVELOPMENT 169 25 0.1479 5.36E−18 7.19E−16 GO_EXTRACELLULAR_MATRIX 428 37 0.0869 5.83E−18 7.65E−16 GO_NEURON_PROJECTION_MORPHOGENESIS 402 36 0.0896 6.17E−18 7.92E−16 GO_REPRODUCTIVE 1297 65 0.0503 7.52E−18 9.51E−16 GO_SKELETAL_SYSTEM_DEVELOPMENT 45

38 0.0835 7.71E−18 9.51E−16

indicates data missing or illegible when filed

TABLE 5 FR Responsive Downregulated Genes GSEA # Genes in # Genes in FDR Gene Set Name Gene Set (K) overlap (k) k/K p-value q-value BENPORATH_ES_WITH_H

K27ME3 1118 112  0.1002 2.12E−59 1.01E−55 BENPORATH_SU212_TARGETS 1038 108  0.1040 7.00E−59 1.67E−55 BENPORATH_

D_TARGETS 1062 10

0.0960 2.97E−5

4.47E−49 MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 1069 95 0.0889 1.08E−

1.29E−42 BENPORATH_PRC2_TARGETS 652 72 0.1104

.

E−41

.67E−3

MIKKELSON_MCV6_HCP_WITH_H3K27ME3 435 4

0.1126 1.82E−28 1.45E−25 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP 425 47 0.11

5.40E−27 3.29E−24 MEISSNER_NPC_HCP_WITH_H3K4ME2 491

0 0.1018 5.52E−27 3.29E−24 MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 349 41 0.1175 1.04E−24

.

E−22 ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY 1725

7 0.0504 7.48E−24 3.58E−21 NABA_MATRISOME 1028

0.0642 9.

E−24 4.17E−21 MARTING_TRETINOIN_RESPONSE_UP 857 60 0.0700 1.5

E−23 6.00E−21 PEREZ_TPS3_TARGETS 1174 70 0.0596 2.66E−23 9.79E−21 DOOD_NASOPHARYNGEAL_CARCINOMA_UP 1821 88 0.0483 7.02E−23 2.40E−20 LEE_BMP2_TARGETS_UP 745 53 0.0733 3.17E−23 1.

1E−18 V

_GASTRIC_CANCER_EARLY_DN 367

0.1

4.85E−21 1.45E−18 MIKKELSEN_MEF_HCP_WTIH_H3K27ME3 5

0 46 0.0780 3.88E−20 1.04E−17 SMIO_BREAST_CANCER_BASAL_DN 701 50 0.0713 3.93E−20 1.04E−17 GOZGIT_ESB1_TARGETS_DN 781 52 0.0

1.38E−19 3.46E−17 MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 210 28 0.1333 9.29E−19 2.16E−16 MEISSNER_BRAIN_HCP_WITH_H3K27ME3 2

9 3

0.1152 9.51E−19 2.16E−16 NARA_CORE_MATRISOME 275 31 0.1127 1.81E−18

.

E−16

_MAIRISOMEWING_SARCOMA_PROGENITOR_UP 430 37 0.08

7.9

E−18 1.

E−15 MIKKELSEN_NPC_HCP_WITH_H3K27ME3 341

0.0

68 1.49E−17 2.97E−15 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN 42

0.08

4.58E−17 8.67E−15 ACEVEDO_FGFR3_TARGETS_IN_PROSTATE_CANCER_MODEL_ON 308 3

0.100

4.72E−17 8.67E−15

_PROSTATE_CANCER_ON 481 38 0.07

4.90E−17 8.67E−15 CHICAS_RBL_TARGETS_CONFLUENT 567 41 0.0723 6.29E−17 1.07E−14 ONDER_CDH1_TARGETS_2_DN 464 37 0.0797 9.42E−17 1.55E−14 GAUSSMANN_MLL_AF4_FUSION_TARGETS_

_UP 185 24 0.1297

.35E−16 8.53E−14 KINSEY_TARGETS_OF_EWSR1_

_FUSION_DN 329 30 0.0

12 2.23E−15

.44E−13 DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN 50

3

0.0713 7.88E−15 1.18E−12 DURAND_SIRCOMA_S_UP 2

7 28 0.0

43 8.28E−15 1.20E−12

AEGER_METASTAS

_DN 2

8 26 0.1008 1.5

E−14 2.19E−12 SMID_BREAST_CANCER_BASAL_UP 648 40 0.0617 2.92E−14 3.

E−12 RODGIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN 637 36 0.0670 5.04E−14

.69E−12 TARTE_PLASMA_CELL_VS_PLASMABLAST_UP 3

0.077

5.65E−14 7.

E−12 YOSHIMURA_MAP

_TARGEST_UP 1305 38 0.0444 8.62E−14 1.08E−11

M_MAMMARY_STEM_CELL_UP 489 34 0.0

9

9.09E−14 1.11E−11 NABA_

M_CLYCOPROTEINS 196 22 0.

1.82E−13 2.18E−11 MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27M3 142 19 0.1

8 3.

7E−13 3.92E−11

_TCF21_TARGETS_2_UP 42

0.0724 3.90E−13 4.43E−11 MASSARWEM_TAMOXIFEN_RESISTANCE_UP

78

0.0623 4.4

E−13 4.9

E−11 WEST_ADRENOCORTICAL_TUMOR_DN 546 34 0.0

23 2.02E−12 2.1

E−10 KAAB_HEART_ATRIUM_VS_VENTRICLE_UP 249 23 0.0924 3.27E−12 3.37E−10 WONG_ADULT_TISSUE_STEM_MODULE 721

0.0

.70E−12 3.84E−10 BRUINS_

VC_RESPONSE_VIA_

_GROUP_A 89

44 0.0490 4.10E−12 4.17E−10 MANALO_HYPOKIA_UP 207 21 0.1014 4.63E−12 4.61E−10

ALOCK_ALZHEIMERS_DISEASE_UP 1

91

0.0378 5.

E−12 5.0

E−10 MSISSNER_NPC_HCP_WITH_

_UNMETHLATED

0.0616 5.80E−12 5.54E−10

indicates data missing or illegible when filed

Example 6: Determine the Therapeutic Benefit in Mouse Models

In this example we will determine whether FR has potential to provide vision sparing therapy for primary (ocular) UM tumors. Treating primary UM tumors via intravitreal rather than systemic administration of FR might provide a more effective and better tolerated means of intervening pharmacologically, because this approach might enable FR to be administered at higher dose. Based on our preliminary studies of UM cells in culture, intravitreal injection might be therapeutically beneficial by inhibiting tumor growth, promoting apoptosis, and/or pushing tumor re-differentiation toward melanocytic phenotypes less likely to metastasize. FR might provide vision-sparing therapy because our preliminary data indicate that it preserves retina structure. Our second priority is to determine whether FR administered systemically could provide therapeutic benefit for metastatic UM tumors. An important goal in both priorities will be to determine whether the effects of FR in models of primary or metastatic UM tumors require reinstatement of PRC2-mediated gene silencing, thereby testing the pathological and therapeutic relevance of the novel signaling mechanism suggested by the studies of human UM cells in culture.

No mouse or other animal model of UM fully recapitulates the disease; instead, various models are used based on the specific questions to be answered. Here we will use two well-accepted mouse models: a transgenic model of primary UM tumors driven by conditional expression of constitutively active Gαq (Q209L) in melanocytes, and an orthotopic transplant model using human UM cell lines and immune deficient (NSG) mice. Also contemplated are PDX models of UM because their tumor cells might better mimic response of human UM tumors to FR.

ERG recordings of intact mice will be used to determine what concentration of intravitreally injected FR affects retina function. One eye will be injected with FR and the other with vehicle as a control. Intravitreal injection itself does not affect retina function as assessed by ERGs. Standard corneal ERGs will be recorded 24 h after injection using scotopic and photopic illumination to identify effects on rod and/or cones, bipolar neurons, or feedback between retinal neurons. ERGs will be recorded weekly thereafter to determine how long the effects of a single FR injection persist. If ERGs do not return to normal, retina histology will be used to assess whether structural defects indicative of cell death have occurred. Although substantial, sustained impairment of retina function would suggest that FR is unlikely to provide vision-sparing therapy of primary UM tumors, this inhibitor could still be therapeutically beneficial if it impairs tumor growth and/or development of metastatic disease.

Next we will determine whether FR targets primary ocular tumors in a transgenic mouse model of UM. These experiments will use the only established transgenic model of UM in which conditional expression of constitutively active Gαq(Q209L) is induced by Mitf-CRE in uveal and other melaoncytes. This model has key advantages over transplant models. First, it is highly penetrant and reproducible. Occular tumors occur in 100% of mice within 4 weeks of age. Second, hematogenous dissemination of tumor cells to the lung occurs in >90% of mice by 3 months of age, making this transgenic model well suited for determining whether FR inhibits metastatic dissemination or growth. Although the transgenic models do not recapitulate other genetic changes characteristic of human UM, it is the only mouse model that produces primary tumors within the same compartment (uveal tract) as in human UM. In contrast, tumor xenografts develop intravitreally are inappropriate for indicating how tumors arising within the uveal tract might respond to FR.

Transgenic uveal melanoma tumors will be imaged non-invasively, by spectral-domain optical coherence tomography (SD-OCT) and angiography. These techniques enable ocular tumor volume and blood supply recruitment to be followed over time. Baseline images will be acquired in 4-week old mice when tumors are small but evident. The next day, vehicle will be injected intravitreally into one eye and FR at various concentrations, as suggested by studies of FR on retina function, into the other eye. The same imaging and intravitreal injection procedures will be repeated one week later; further injections will not be performed because they would damage the eye. Final tumor images will be acquired in 6-week old mice (i.e. one week after, the 2nd FR or vehicle injection), by which time control tumors have expanded to occupy—30% of the intravitreal space. Inhibition of tumor growth as a function of FR concentration will be determined. Tumors will be harvested and analyzed by immunoblotting or immunohistochemistry for the activity state of signaling pathways downstream of constitutively active Gαq/11 in UM (YAP; MEK), to determine dose of FR is sufficient to inhibit constitutively active Gαq signaling in tumors.

Next we will determine whether treatment reinstates PRC2-mediated repression in primary ocular tumors and whether this mechanism is required for FR to inhibit tumor growth. RNA-Seq will be performed to determine whether intraocular injection of FR in the transgenic model of UM reinstates PRC2-mediated repression. Second, we will determine whether maintaining PRC2 in an inactive state with an Ezh1/2 inhibitor (GSK503) interferes with the ability of FR to blunt tumor growth and/or reinstate PRC2-mediated silencing. Using the same schedule involving two weekly intravitreal injections described in above, vehicle or FR at its effective concentration will be co-injected with GSK503 at a concentration known to inactivate the catalytic subunits of PRC2 complexes in vivo. Tumor growth will be imaged by SD-OCT. PRC2 inhibition in ocular tumors will be detected by immunoblotting for histone H3K27me3 normalized to total histone H3. The effects of FR injected with or without GSK503 on expression of PRC2 target genes will be determined by RNA-Seq. Based on our studies of human UM cells, it is expected that FR will reinstate silencing of PRC2-regulated genes in transgenic UM tumors, whereas this effect of FR will be blocked or blunted by inhibition of Ezh1/2.

Determine whether FR inhibits development of lung metastases in the transgenic UM model. This question will be addressed in two ways, both of which will examine the appearance of pigmented lung lesions in 3-month old transgenic mice, which normally occur with high penetrance by this time point. We will determine whether FR administered systemically by daily subcutaneous injection (0.1-0.3 mg/kg) affects the growth of primary ocular tumors and/or lung lesions the transgenic model.

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1. A method of allosterically inhibiting nucleotide exchange of a constitutively active G protein α-subunit in a cell by trapping the G protein α-subunit in a GDP-bound state, method comprising: contacting the cell with an effective amount of

or a derivative thereof, wherein the effective amount allosterically inhibits GDP release from the G protein α-subunit.
 2. The method of claim 1, wherein said GDP bound constitutively active Gα subunit assembles into Gαβγ heterotrimers, further suppressing GDP release and stabilizing the heterotrimer in an inactive state.
 3. The method of claim 1, wherein contacting the cell occurs in vitro, in vivo or ex vivo.
 4. The method of claim 1, wherein the cell is in a subject having or suspected of having a disease or disorder associated with constitutively active G-protein signaling and FR900359, YM-254890 is administered at a dose between 0.1 to 0.3 mg/kg.
 5. (canceled)
 6. The method of claim 2, wherein stabilizing the Gαβγ heterotrimer in an inactive state reduces a downstream constituently active G-protein signaling pathway, wherein the downstream signaling pathways include Yes-associated protein (YAP) activity, adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) or p38 MAPK.
 7. The method of claim 4, wherein the disease or disorder associated with constitutively active G-protein signaling is selected from growth hormone-secreting pituitary tumors, tumors derived from Nevus of Ota, colon cancer, lung cancer, adenocarcinoma, skin melanoma, thyroid adenoma, cholera, and Sturge-Weber Syndrome.
 8. (canceled)
 9. A method of treating uveal melanoma in a subject in need thereof, method comprising: administering to the subject a composition comprising a dose of about 0.1 mg/kg to about 0.3 mg/kg of

or a derivative thereof, wherein the effective amount allosterically inhibits GDP release from an constitutively active G protein α-subunit.
 10. The method of claim 9, wherein the FR900359, YM-254890, or a derivative thereof down-regulates constitutively active G-protein signaling.
 11. The method of claim 9, wherein uveal melanoma cell proliferation is reduced relatively to untreated uveal melanoma cells.
 12. (canceled)
 13. The method of claim 9, wherein

the uveal melanoma cells re-differentiate compared to untreated uveal melanoma cells.
 14. The method of claim 13, wherein re-differentiation is determined by loss of spindle morphology, flatting of the cell, production of multiple projections, increased melanocytic pigmentation or combinations thereof.
 15. The method of claim 13, wherein genes targeted by the polycomb repressive complex 2 (PRC2) are repressed.
 16. The method of claim 15, wherein the repressed genes ADRA2A (alpha-adrenergic receptor-2A) and HAND2 (heart and neural crest derivatives expressed-2).
 17. A method of treatment of a disease, disorder, or condition associated with constitutively active G protein signaling in a subject in need thereof, the method comprising: administering to the subject a composition comprising a dose of about 0.1 mg/kg to about 0.3 mg/kg of

or a derivative thereof; wherein, the therapeutically effective amount reduces or prevents constitutively active G protein signaling.
 18. The method of claim 17, wherein the disease, disorder, or condition is selected from growth hormone-secreting pituitary tumors, tumors derived from Nevus of Ota, constitutively active G protein mediated cancer (e.g. colon, lung, adenocarcinoma, skin melanoma, thyroid adenomas), cholera, and Sturge-Weber Syndrome 19.-20. (canceled)
 21. The method of claim 17, wherein the effective amount allosterically inhibits GDP release from the G protein α-subunit.
 22. The method of claim 17, wherein the disorder, or condition associated with constitutively active G protein signaling is a tumor or cancer and tumor or cancer cell growth is reduced relative to the untreated tumor or cancer cell.
 23. The method of claim 17, wherein the disorder, or condition associated with constitutively active G protein signaling is a tumor or cancer and tumor or cancer metastasis is reduced relative to the untreated tumor or cancer cell. 